answerals.vcfannotate.samples_no_variants = answerals.metadata$dataset_sample[!answerals.metadata$dataset_sample %in% answerals.vcfannotate$dataset_sample] # 0 i.e. all samples have at least 1 variant
answerals.vcfannotate.totals = answerals.vcfannotate %>% distinct(dataset_sample, .keep_all = TRUE) #keep 1 row per sample for total number of variants
# generalised linear model spline
answerals.vcfannotate.totals.glm = glm(data=answerals.vcfannotate.totals, total ~ CONDITION + rms::rcs(total_reads, 3), family = poisson)
summary(answerals.vcfannotate.totals.glm)##
## Call:
## glm(formula = total ~ CONDITION + rms::rcs(total_reads, 3), family = poisson,
## data = answerals.vcfannotate.totals)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -20.100 -6.822 -2.358 2.699 48.785
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.063e+01 3.409e-03 3119.19 <2e-16 ***
## CONDITIONALS 1.020e-02 7.027e-04 14.52 <2e-16 ***
## rms::rcs(total_reads, 3)total_reads 4.116e-09 4.353e-11 94.54 <2e-16 ***
## rms::rcs(total_reads, 3)total_reads' -2.174e-09 5.152e-11 -42.20 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 54707 on 279 degrees of freedom
## Residual deviance: 36003 on 276 degrees of freedom
## AIC: 39600
##
## Number of Fisher Scoring iterations: 3
# Coefficients:
# Estimate Std. Error z value Pr(>|z|)
# (Intercept) 1.063e+01 3.409e-03 3119.19 <2e-16 ***
# CONDITIONALS 1.020e-02 7.027e-04 14.52 <2e-16 ***
# Violin total variant events
answerals.vcfannotate.totals.stats = tibble(group1 = "CTRL", group2 = "ALS", p.signif = "****", y.position = 75000, xmin = 1, xmax = 2)
answerals.vcfannotate.total.violin <- violin_plot(answerals.vcfannotate.totals, color_by = "CONDITION", continuous = "total", cols = c("dodgerblue2", "firebrick2"), one_sample = FALSE, plot_stats = FALSE, arrow_labels = FALSE, ylims = c(50000,76000), dpi = 72, ylabel = "Total Number of Variants", title = "All Variant types") +
stat_pvalue_manual(answerals.vcfannotate.totals.stats, tip.length = 0.01, size = 4)
answerals.vcfannotate.total.violinanswerals.vcfannotate.snp = answerals.vcfannotate %>% filter(variant_type == "SNP")
# add samples with 0 variants for each variant type
samples_no_SNP = answerals.metadata$dataset_sample[!answerals.metadata$dataset_sample %in% pull(answerals.vcfannotate.snp,dataset_sample)]
answerals.vcfannotate.snp.glm = glm(data = answerals.vcfannotate.snp, n ~ CONDITION + rms::rcs(total_reads, 3), family = poisson)
summary(answerals.vcfannotate.snp.glm)##
## Call:
## glm(formula = n ~ CONDITION + rms::rcs(total_reads, 3), family = poisson,
## data = answerals.vcfannotate.snp)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -18.267 -6.464 -2.250 2.197 46.466
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.048e+01 3.680e-03 2847.29 <2e-16 ***
## CONDITIONALS 8.880e-03 7.581e-04 11.71 <2e-16 ***
## rms::rcs(total_reads, 3)total_reads 4.164e-09 4.700e-11 88.61 <2e-16 ***
## rms::rcs(total_reads, 3)total_reads' -2.299e-09 5.564e-11 -41.33 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 48499 on 279 degrees of freedom
## Residual deviance: 32867 on 276 degrees of freedom
## AIC: 36421
##
## Number of Fisher Scoring iterations: 3
# Coefficients:
# Estimate Std. Error z value Pr(>|z|)
# (Intercept) 1.048e+01 3.680e-03 2847.29 <2e-16 ***
# CONDITIONALS 8.880e-03 7.581e-04 11.71 <2e-16 ***
answerals.vcfannotate.snp.stats = tibble(group1 = "CTRL", group2 = "ALS", p.signif = "****", y.position = 62000, xmin = 1, xmax = 2)
answerals.vcfannotate.snp.violin <- violin_plot(answerals.vcfannotate.snp, color_by = "CONDITION", continuous = "n", cols = c("dodgerblue2", "firebrick2"), plot_stats = FALSE, arrow_labels = FALSE, ylims = c(40000,64000), dpi = 72, ylabel = "Number of Variants", title = "SNV") +
stat_pvalue_manual(answerals.vcfannotate.snp.stats, tip.length = 0.01, size = 4)
answerals.vcfannotate.snp.violinanswerals.vcfannotate.insertion = answerals.vcfannotate %>% filter(variant_type == "Insertion")
# add samples with 0 variants for each variant type
samples_no_Insertion = answerals.metadata$dataset_sample[!answerals.metadata$dataset_sample %in% pull(answerals.vcfannotate.insertion,dataset_sample)]
answerals.vcfannotate.Insertion.glm = glm(data = answerals.vcfannotate.insertion, n ~ CONDITION + rms::rcs(total_reads, 3), family = poisson)
summary(answerals.vcfannotate.Insertion.glm)##
## Call:
## glm(formula = n ~ CONDITION + rms::rcs(total_reads, 3), family = poisson,
## data = answerals.vcfannotate.insertion)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -15.4957 -2.8982 -0.3836 3.0568 20.8196
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 8.121e+00 1.219e-02 666.031 < 2e-16 ***
## CONDITIONALS 1.928e-02 2.528e-03 7.624 2.47e-14 ***
## rms::rcs(total_reads, 3)total_reads 3.391e-09 1.557e-10 21.781 < 2e-16 ***
## rms::rcs(total_reads, 3)total_reads' -6.114e-10 1.837e-10 -3.329 0.000873 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 9242.2 on 279 degrees of freedom
## Residual deviance: 7330.3 on 276 degrees of freedom
## AIC: 10212
##
## Number of Fisher Scoring iterations: 3
# Coefficients:
# Estimate Std. Error z value Pr(>|z|)
# (Intercept) 8.121e+00 1.219e-02 666.031 < 2e-16 ***
# CONDITIONALS 1.928e-02 2.528e-03 7.624 2.47e-14 ***
answerals.vcfannotate.insertion.stats = tibble(group1 = "CTRL", group2 = "ALS", p.signif = "****", y.position = 6400, xmin = 1, xmax = 2)
answerals.vcfannotate.insertion.violin <- violin_plot(answerals.vcfannotate.insertion, color_by = "CONDITION", continuous = "n", cols = c("dodgerblue2", "firebrick2"), plot_stats = FALSE, arrow_labels = FALSE, ylims = c(3500,6700), dpi = 72, ylabel = "", title = "Insertion") +
stat_pvalue_manual(answerals.vcfannotate.insertion.stats, tip.length = 0.01, size = 4)
answerals.vcfannotate.insertion.violinanswerals.vcfannotate.deletion = answerals.vcfannotate %>% filter(variant_type == "Deletion")
samples_no_Deletion = answerals.metadata$dataset_sample[!answerals.metadata$dataset_sample %in% pull(answerals.vcfannotate.deletion,dataset_sample)]
answerals.vcfannotate.Deletion.glm = glm(data = answerals.vcfannotate.deletion, n ~ CONDITION + rms::rcs(total_reads, 3), family=poisson)
summary(answerals.vcfannotate.Deletion.glm)##
## Call:
## glm(formula = n ~ CONDITION + rms::rcs(total_reads, 3), family = poisson,
## data = answerals.vcfannotate.deletion)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -6.5241 -1.4909 -0.2659 0.8584 9.7615
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 7.858e+00 1.351e-02 581.45 < 2e-16 ***
## CONDITIONALS 1.701e-02 2.789e-03 6.10 1.06e-09 ***
## rms::rcs(total_reads, 3)total_reads 4.337e-09 1.726e-10 25.13 < 2e-16 ***
## rms::rcs(total_reads, 3)total_reads' -2.406e-09 2.041e-10 -11.79 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 3408.5 on 279 degrees of freedom
## Residual deviance: 2102.7 on 276 degrees of freedom
## AIC: 4929
##
## Number of Fisher Scoring iterations: 3
# Coefficients:
# Estimate Std. Error z value Pr(>|z|)
# (Intercept) 7.858e+00 1.351e-02 581.45 < 2e-16 ***
# CONDITIONALS 1.701e-02 2.789e-03 6.10 1.06e-09 ***
answerals.vcfannotate.insertion.stats = tibble(group1 = "CTRL", group2 = "ALS", p.signif = "****", y.position = 4900, xmin = 1, xmax = 2)
answerals.vcfannotate.deletion.violin <- violin_plot(answerals.vcfannotate.deletion, color_by = "CONDITION", continuous = "n", cols = c("dodgerblue2", "firebrick2"), plot_stats = FALSE, arrow_labels = FALSE, ylims = c(3000,5000), dpi = 72, ylabel = "", title = "Deletion") +
stat_pvalue_manual(answerals.vcfannotate.insertion.stats, tip.length = 0.01, size = 4)
answerals.vcfannotate.deletion.violinlibrary(MutationalPatterns)
ref_genome <- "BSgenome.Hsapiens.UCSC.hg38"
library(ref_genome, character.only = TRUE)
type_occurrences = readRDS(here(shared_path, "answerals/rnavar/mutationalpatterns/type_occurrences.RDS"))
answerals.multiqc_rseqc_read_distribution.tsv = read_tsv(here(shared_path,"answerals/nfcore/multiqc/star_salmon/multiqc_data/multiqc_rseqc_read_distribution.txt"), show_col_types = FALSE) %>% clean_names()
answerals.base_substitutions = type_occurrences %>% as_tibble(rownames = "sample") %>% select(-`C>T at CpG`, -`C>T other`) %>%
left_join(select(answerals.metadata, sample, condition)) %>%
pivot_longer(!c(condition, sample), names_to = "Substitution", values_to = "count") %>%
mutate(CONDITION = factor(toupper(condition), levels = c("CTRL","ALS")), Substitution = as.factor(Substitution)) %>%
left_join(select(answerals.multiqc_rseqc_read_distribution.tsv, sample, total_reads))
# ### C>A
# glm_starfusion_C_A = glm(data = filter(answerals.base_substitutions, Substitution == "C>A"), count ~ CONDITION + rms::rcs(total_reads, 3), family=poisson)
# summary(glm_starfusion_C_A)
# # Coefficients:
# # Estimate Std. Error z value Pr(>|z|)
# # (Intercept) 7.672e+00 1.443e-02 531.861 < 2e-16 ***
# # CONDITIONALS 8.564e-03 2.952e-03 2.901 0.00372 **
#
# ### C>G
# glm_starfusion_C_G = glm(data = filter(answerals.base_substitutions, Substitution == "C>G"), count ~ CONDITION + rms::rcs(total_reads, 3), family=poisson)
# summary(glm_starfusion_C_G)
# # Coefficients:
# # Estimate Std. Error z value Pr(>|z|)
# # (Intercept) 8.085e+00 1.230e-02 657.069 <2e-16 ***
# # CONDITIONALS 3.246e-03 2.533e-03 1.281 0.2
#
# ### C>T
# glm_starfusion_C_T = glm(data = filter(answerals.base_substitutions, Substitution == "C>T"), count ~ CONDITION + rms::rcs(total_reads, 3), family=poisson)
# summary(glm_starfusion_C_T)
# # Coefficients:
# # Estimate Std. Error z value Pr(>|z|)
# # (Intercept) 9.365e+00 6.467e-03 1448.230 < 2e-16 ***
# # CONDITIONALS 4.251e-03 1.331e-03 3.193 0.00141 **
#
# ### T>A
# glm_starfusion_T_A = glm(data = filter(answerals.base_substitutions, Substitution == "T>A"), count ~ CONDITION + rms::rcs(total_reads, 3), family=poisson)
# summary(glm_starfusion_T_A)
# # Coefficients:
# # Estimate Std. Error z value Pr(>|z|)
# # (Intercept) 7.247e+00 1.803e-02 401.926 < 2e-16 ***
# # CONDITIONALS 1.202e-02 3.700e-03 3.247 0.00117 **
#
# ### T>C
# glm_starfusion_T_C = glm(data = filter(answerals.base_substitutions, Substitution == "T>C"), count ~ CONDITION + rms::rcs(total_reads, 3), family=poisson)
# summary(glm_starfusion_T_C)
# # Coefficients:
# # Estimate Std. Error z value Pr(>|z|)
# # (Intercept) 9.563e+00 5.869e-03 1629.54 <2e-16 ***
# # CONDITIONALS 1.433e-02 1.214e-03 11.81 <2e-16 ***
#
# ### T>G
# glm_starfusion_T_G = glm(data = filter(answerals.base_substitutions, Substitution == "T>G"), count ~ CONDITION + rms::rcs(total_reads, 3), family=poisson)
# summary(glm_starfusion_T_G)
# # Coefficients:
# # Estimate Std. Error z value Pr(>|z|)
# # (Intercept) 7.741e+00 1.456e-02 531.774 <2e-16 ***
# # CONDITIONALS 2.634e-03 2.995e-03 0.879 0.379
ipsc_mn_als_datasets.Substitution.stat <- answerals.base_substitutions %>% group_by(Substitution) %>% t_test(count ~ CONDITION) %>% mutate(p.signif = c("**","ns","**","**","****","ns"), y.position = c(4500,5500,20500,2700,25000,3900))
# ipsc_mn_als_datasets.Substitution.stat
# # Substitution .y. group1 group2 n1 n2 statistic df p p.signif y.position
# # <fct> <chr> <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <chr> <dbl>
# # 1 C>A count CTRL ALS 42 238 -2.14 59.5 0.0362 ** 4500
# # 2 C>G count CTRL ALS 42 238 -1.77 62.4 0.0812 ns 5500
# # 3 C>T count CTRL ALS 42 238 -1.86 63.6 0.0672 ** 20500
# # 4 T>A count CTRL ALS 42 238 -2.27 56.2 0.0269 ** 2700
# # 5 T>C count CTRL ALS 42 238 -2.23 56.0 0.0294 **** 25000
# # 6 T>G count CTRL ALS 42 238 -1.86 63.8 0.0674 ns 3900
answerals.base_substitutions.violin <- ggplot(answerals.base_substitutions, aes(x = CONDITION, y = count, colour = CONDITION)) +
ggrastr::rasterise(geom_violin(adjust = 1), dpi = 72) +
ggrastr::rasterise(geom_sina(size = 0.5), dpi = 72) +
ggrastr::rasterise(geom_boxplot(aes(fill = CONDITION), colour = "black", width=0.2, alpha = 0.5, outlier.shape = NA), dpi = 72) +
scale_colour_manual(values = c("dodgerblue2", "firebrick2")) + scale_fill_manual(values = c("dodgerblue2", "firebrick2")) +
theme_oz() + theme(legend.position = "none", plot.title = element_text(hjust = 0.5), plot.subtitle = element_text(hjust = 0.5), panel.border = element_blank(), axis.ticks = element_line(colour = "black") ) +
facet_wrap(~ Substitution, scales = "free", nrow = 2) + labs(y = "Number of Variants", x = "") + #, title = "Base substitution types"
stat_pvalue_manual(ipsc_mn_als_datasets.Substitution.stat, label = "p.signif", tip.length = 0.01, size = 4, hide.ns = TRUE)
answerals.base_substitutions.violinipsc_mn_als_datasets.starfusion.als_events <- ipsc_mn_als_datasets.starfusion %>% filter(condition == "als") %>% distinct(fusion_name) %>% pull(fusion_name)
ipsc_mn_als_datasets.starfusion.ctrl_events <- ipsc_mn_als_datasets.starfusion %>% filter(condition == "ctrl") %>% distinct(fusion_name) %>% pull(fusion_name)
ipsc_mn_als_datasets.starfusion.als_ctrl_events <- list("ALS" = ipsc_mn_als_datasets.starfusion.als_events, "CTRL" = ipsc_mn_als_datasets.starfusion.ctrl_events)
ipsc_mn_als_datasets.starfusion.als_ctrl_events_venn <- ggvenn(ipsc_mn_als_datasets.starfusion.als_ctrl_events, fill_color = c("firebrick2", "dodgerblue2"), set_name_color = c("firebrick2", "dodgerblue2"), show_percentage = FALSE, stroke_size = 0.4, set_name_size = 3.5) + labs(subtitle = "Unique Gene Fusions") +
theme(plot.subtitle = element_text(hjust = 0.5, size = 9), plot.margin = unit(c(0, -1, 0, -1), "lines"))
ipsc_mn_als_datasets.starfusion.als_ctrl_events_vennipsc_mn_als_datasets.starfusion.n = ipsc_mn_als_datasets.starfusion %>%
add_count(dataset_sample) %>% # count number of fusions per sample
distinct(dataset_sample, .keep_all = TRUE) %>% select(dataset_sample, n, CONDITION, dataset, total_reads) #keep 1 row per sample
# add samples with 0 fusions
ipsc_mn_als_datasets.starfusion.samples_no_fusions = ipsc_mn_als_datasets.paired_end.metadata$dataset_sample[!ipsc_mn_als_datasets.paired_end.metadata$dataset_sample %in% ipsc_mn_als_datasets.starfusion.n$dataset_sample] # "smith_tardbp_1" "smith_ctrl_1" 0 events
ipsc_mn_als_datasets.paired_end.metadata.no_fusions = ipsc_mn_als_datasets.paired_end.metadata %>% filter(dataset_sample %in% ipsc_mn_als_datasets.starfusion.samples_no_fusions) %>%
left_join(multiqc_rseqc_read_distribution.tsv) %>%
mutate(CONDITION = factor(toupper(condition), levels = c("CTRL","ALS")), n = 0) %>% select(dataset_sample, n, CONDITION, dataset, total_reads)
ipsc_mn_als_datasets.starfusion.n = bind_rows(ipsc_mn_als_datasets.starfusion.n, ipsc_mn_als_datasets.paired_end.metadata.no_fusions)
glm_starfusion = glm(data = ipsc_mn_als_datasets.starfusion.n, n ~ CONDITION + dataset + rms::rcs(total_reads, 3), family=poisson)
summary(glm_starfusion)##
## Call:
## glm(formula = n ~ CONDITION + dataset + rms::rcs(total_reads,
## 3), family = poisson, data = ipsc_mn_als_datasets.starfusion.n)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -3.7724 -1.0338 -0.2193 0.6234 5.8605
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.121e+00 3.330e-01 6.369 1.90e-10 ***
## CONDITIONALS 1.327e-01 4.282e-02 3.098 0.00195 **
## datasetcatanese -2.166e-01 1.355e-01 -1.599 0.10981
## datasetdafinca.c9orf72 -1.340e+00 2.147e-01 -6.243 4.30e-10 ***
## datasetdafinca.tardbp -4.989e-01 2.798e-01 -1.783 0.07455 .
## datasetdesantis -5.775e-01 2.751e-01 -2.099 0.03584 *
## datasetkiskinis 7.013e-01 2.969e-01 2.362 0.01816 *
## datasetneurolincs.diMN -4.582e-01 6.999e-02 -6.546 5.90e-11 ***
## datasetneurolincs.iMN -8.916e-01 1.271e-01 -7.016 2.28e-12 ***
## datasetsmith -2.752e+00 6.484e-01 -4.244 2.20e-05 ***
## datasetsommer -1.106e+00 1.971e-01 -5.614 1.98e-08 ***
## datasetwang 3.354e-01 2.454e-01 1.367 0.17173
## rms::rcs(total_reads, 3)total_reads 5.115e-09 4.914e-09 1.041 0.29785
## rms::rcs(total_reads, 3)total_reads' -7.908e-09 3.231e-09 -2.447 0.01439 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 1202.77 on 395 degrees of freedom
## Residual deviance: 747.06 on 382 degrees of freedom
## AIC: 2356.8
##
## Number of Fisher Scoring iterations: 4
# Coefficients:
# Estimate Std. Error z value Pr(>|z|)
# (Intercept) 2.121e+00 3.330e-01 6.369 1.90e-10 ***
# CONDITIONALS 1.327e-01 4.282e-02 3.098 0.00195 **
ipsc_mn_als_datasets.starfusion.n.stats = tibble(group1 = "CTRL", group2 = "ALS", p.signif = "**", y.position = 40, xmin = 1, xmax = 2)
ipsc_mn_als_datasets.starfusion.violin <- violin_plot(ipsc_mn_als_datasets.starfusion.n, color_by = "CONDITION", continuous = "n", cols = c("dodgerblue2", "firebrick2"), plot_stats = FALSE, arrow_labels = FALSE, ylims = c(0,42), dpi = 72, ylabel = "Number of Fusion Events", title = "All Fusion types") +
stat_pvalue_manual(ipsc_mn_als_datasets.starfusion.n.stats, tip.length = 0.01, size = 4)
ipsc_mn_als_datasets.starfusion.violinanswerals.vcfannotate.s8 = answerals.vcfannotate %>% select(dataset, sample, n, variant_type, condition, mutation, Total = total) %>%
pivot_wider(names_from = "variant_type", values_from = "n", values_fill = 0) %>%
select(dataset, sample, condition, mutation, Total, SNP, Insertion, Deletion) %>% #, Complex
arrange(condition)
kbl(answerals.vcfannotate.s8) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), fixed_thead = T) %>% scroll_box(width = "100%", height = "500px")| dataset | sample | condition | mutation | Total | SNP | Insertion | Deletion |
|---|---|---|---|---|---|---|---|
| answerals | CASE_NEUDE902GCT | als | c9orf72 | 56617 | 48220 | 4710 | 3675 |
| answerals | CASE_NEUAA599TMX | als | sporadic | 56584 | 48981 | 3870 | 3725 |
| answerals | CASE_NEUAB000NKC | als | c9orf72 | 56355 | 48388 | 4636 | 3326 |
| answerals | CASE_NEUAE228FF6 | als | sporadic | 56503 | 48530 | 4342 | 3623 |
| answerals | CASE_NEUAE993EPR | als | sporadic | 70176 | 60471 | 5233 | 4453 |
| answerals | CASE_NEUAF553MJ3 | als | sporadic | 57107 | 49228 | 4267 | 3603 |
| answerals | CASE_NEUAG241NUD | als | sporadic | 57675 | 49382 | 4400 | 3885 |
| answerals | CASE_NEUAG603XLK | als | pfn1 | 47174 | 40535 | 3639 | 2994 |
| answerals | CASE_NEUAG766ULB | als | sporadic | 60427 | 51744 | 4934 | 3742 |
| answerals | CASE_NEUAL076FCE | als | sporadic | 59793 | 50869 | 4989 | 3924 |
| answerals | CASE_NEUAM655HF7 | als | sporadic | 55081 | 47208 | 4230 | 3634 |
| answerals | CASE_NEUAP285GGU | als | sporadic | 56688 | 48716 | 4429 | 3537 |
| answerals | CASE_NEUAT234RK6 | als | sporadic | 57608 | 49123 | 4986 | 3488 |
| answerals | CASE_NEUAW157NMJ | als | sporadic | 58189 | 50092 | 4436 | 3653 |
| answerals | CASE_NEUAW717TN6 | als | sporadic | 57854 | 49562 | 4370 | 3910 |
| answerals | CASE_NEUAX665ZHY | als | sporadic | 57161 | 48894 | 4469 | 3789 |
| answerals | CASE_NEUAY067UTB | als | chchd1 | 60322 | 51828 | 4567 | 3919 |
| answerals | CASE_NEUAZ394JEZ | als | sporadic | 62141 | 53706 | 4534 | 3890 |
| answerals | CASE_NEUBA169GXD | als | sporadic | 60349 | 51652 | 4797 | 3890 |
| answerals | CASE_NEUBC901KL3 | als | sporadic | 60956 | 51771 | 5372 | 3807 |
| answerals | CASE_NEUBC998WWB | als | sqstm1 | 59342 | 50924 | 4598 | 3813 |
| answerals | CASE_NEUBD218YR3 | als | fig4 | 56370 | 48129 | 4615 | 3614 |
| answerals | CASE_NEUBD288RXQ | als | sporadic | 55161 | 47418 | 4097 | 3639 |
| answerals | CASE_NEUBK117YXL | als | sporadic | 59463 | 51145 | 4665 | 3643 |
| answerals | CASE_NEUBM949LA5 | als | sporadic | 58583 | 50142 | 4614 | 3812 |
| answerals | CASE_NEUBN979ZZ5 | als | sporadic | 61495 | 52837 | 4928 | 3722 |
| answerals | CASE_NEUBT273FH3 | als | sporadic | 56265 | 48124 | 4487 | 3646 |
| answerals | CASE_NEUBW008RJ5 | als | sporadic | 61206 | 52495 | 4727 | 3979 |
| answerals | CASE_NEUBY734PFR | als | sporadic | 55299 | 47536 | 4173 | 3585 |
| answerals | CASE_NEUCB613CA9 | als | sporadic | 58135 | 49890 | 4495 | 3741 |
| answerals | CASE_NEUCD502BFU | als | sod1 | 60442 | 51808 | 4904 | 3719 |
| answerals | CASE_NEUCE965ZGK | als | c9orf72 | 57625 | 49386 | 4460 | 3771 |
| answerals | CASE_NEUCF538BRM | als | sporadic | 58487 | 49990 | 4721 | 3769 |
| answerals | CASE_NEUCG511MJ6 | als | sporadic | 61314 | 52448 | 5018 | 3828 |
| answerals | CASE_NEUCN596RR3 | als | sporadic | 57637 | 49881 | 4177 | 3570 |
| answerals | CASE_NEUCP218XVV | als | sporadic | 62812 | 54049 | 4920 | 3829 |
| answerals | CASE_NEUCT022VTK | als | sporadic | 60493 | 51793 | 4646 | 4042 |
| answerals | CASE_NEUCT842RJV | als | sod1 | 58214 | 49653 | 4894 | 3657 |
| answerals | CASE_NEUCU076ADN | als | sporadic | 61936 | 53586 | 4432 | 3905 |
| answerals | CASE_NEUCU245GBQ | als | sporadic | 55305 | 47118 | 4599 | 3578 |
| answerals | CASE_NEUCV578DFJ | als | sporadic | 56700 | 48860 | 4347 | 3484 |
| answerals | CASE_NEUDD018KAH | als | sporadic | 55104 | 47304 | 4203 | 3584 |
| answerals | CASE_NEUDG000ZG5 | als | sporadic | 57075 | 49593 | 3882 | 3597 |
| answerals | CASE_NEUDG272XWC | als | sporadic | 57736 | 49728 | 4263 | 3738 |
| answerals | CASE_NEUDH063DEA | als | sporadic | 56071 | 47885 | 4555 | 3621 |
| answerals | CASE_NEUDM949BAR | als | sporadic | 69775 | 60555 | 4968 | 4236 |
| answerals | CASE_NEUDP155HFH | als | sporadic | 60357 | 51432 | 4971 | 3944 |
| answerals | CASE_NEUDT709YHN | als | c9orf72 | 56328 | 48912 | 3862 | 3550 |
| answerals | CASE_NEUDY534KGP | als | sporadic | 60624 | 51916 | 4824 | 3870 |
| answerals | CASE_NEUDZ473EGM | als | c9orf72 | 61242 | 52126 | 5334 | 3775 |
| answerals | CASE_NEUEB422WW0 | als | sporadic | 60128 | 51463 | 4794 | 3861 |
| answerals | CASE_NEUEC400NYR | als | setx | 59892 | 51429 | 4475 | 3977 |
| answerals | CASE_NEUEK191WYC | als | sporadic | 57379 | 49199 | 4465 | 3707 |
| answerals | CASE_NEUEM029XXZ | als | sporadic | 56477 | 48694 | 4220 | 3552 |
| answerals | CASE_NEUEM720BUU | als | c9orf72 | 54756 | 46712 | 4925 | 3114 |
| answerals | CASE_NEUEN017PCJ | als | sporadic | 59090 | 50634 | 4675 | 3777 |
| answerals | CASE_NEUEN476CLW | als | c9orf72 | 57817 | 49656 | 4548 | 3610 |
| answerals | CASE_NEUET072VDG | als | sporadic | 60255 | 51758 | 4671 | 3822 |
| answerals | CASE_NEUEU318NY2 | als | sporadic | 59240 | 50849 | 4534 | 3848 |
| answerals | CASE_NEUEU558MNK | als | sporadic | 57011 | 48900 | 4349 | 3756 |
| answerals | CASE_NEUEY478NZP | als | sod1 | 60025 | 51188 | 4967 | 3857 |
| answerals | CASE_NEUFB989DT1 | als | sporadic | 57424 | 49535 | 4190 | 3690 |
| answerals | CASE_NEUFH122WN7 | als | sqstm1 | 60603 | 52149 | 4532 | 3907 |
| answerals | CASE_NEUFH461AAN | als | sporadic | 68843 | 59569 | 4938 | 4322 |
| answerals | CASE_NEUFU395MJD | als | sporadic | 56093 | 48085 | 4401 | 3600 |
| answerals | CASE_NEUFV237VCZ | als | c9orf72 | 56842 | 48626 | 4510 | 3700 |
| answerals | CASE_NEUFX386KMB | als | sporadic | 58198 | 49094 | 5283 | 3813 |
| answerals | CASE_NEUFY342UNG | als | sporadic | 58116 | 50159 | 4073 | 3874 |
| answerals | CASE_NEUGD965XVD | als | sporadic | 60862 | 52133 | 4767 | 3955 |
| answerals | CASE_NEUGE540TC4 | als | sporadic | 53921 | 46403 | 4014 | 3495 |
| answerals | CASE_NEUGH995TFK | als | c9orf72 | 61513 | 52988 | 4649 | 3868 |
| answerals | CASE_NEUGJ081HKR | als | c9orf72 | 55208 | 47517 | 4172 | 3514 |
| answerals | CASE_NEUGL543NJ1 | als | sporadic | 57839 | 49612 | 4487 | 3733 |
| answerals | CASE_NEUGP781PDU | als | sporadic | 56686 | 48624 | 4368 | 3685 |
| answerals | CASE_NEUGR121TFD | als | sporadic | 69750 | 60168 | 5084 | 4486 |
| answerals | CASE_NEUGR539MVT | als | sporadic | 58504 | 50015 | 4595 | 3881 |
| answerals | CASE_NEUGW326BRV | als | sporadic | 52833 | 45536 | 4027 | 3265 |
| answerals | CASE_NEUGW340YEB | als | sporadic | 60711 | 52631 | 4259 | 3810 |
| answerals | CASE_NEUHB491NGF | als | sporadic | 58510 | 50251 | 4430 | 3820 |
| answerals | CASE_NEUHG644RYB | als | sporadic | 59879 | 51759 | 4296 | 3816 |
| answerals | CASE_NEUHG791RV5 | als | sporadic | 56657 | 48931 | 4109 | 3614 |
| answerals | CASE_NEUHK991AVP | als | sod1 | 57556 | 49162 | 4595 | 3790 |
| answerals | CASE_NEUHL999WWT | als | sporadic | 57573 | 49110 | 4678 | 3779 |
| answerals | CASE_NEUHM532NDD | als | sporadic | 60699 | 52285 | 4581 | 3828 |
| answerals | CASE_NEUHT569HT1 | als | sporadic | 62072 | 53367 | 4747 | 3951 |
| answerals | CASE_NEUHV216EHA | als | sporadic | 57938 | 49858 | 4351 | 3717 |
| answerals | CASE_NEUHW530WD8 | als | sporadic | 60842 | 52228 | 4727 | 3878 |
| answerals | CASE_NEUHW590KBH | als | sporadic | 54091 | 46700 | 4011 | 3373 |
| answerals | CASE_NEUHY206ZEQ | als | sporadic | 55933 | 47862 | 4431 | 3626 |
| answerals | CASE_NEUHZ302VU4 | als | sporadic | 53741 | 46046 | 4170 | 3519 |
| answerals | CASE_NEUJA217MTJ | als | sporadic | 59038 | 51588 | 3935 | 3508 |
| answerals | CASE_NEUJA666PYD | als | sporadic | 57285 | 49098 | 4458 | 3718 |
| answerals | CASE_NEUJC191RLE | als | pfn1 | 57936 | 49894 | 4339 | 3693 |
| answerals | CASE_NEUJG311WGV | als | sporadic | 57839 | 49407 | 4710 | 3712 |
| answerals | CASE_NEUJG885PY7 | als | sporadic | 60245 | 51768 | 4580 | 3889 |
| answerals | CASE_NEUJH197AK2 | als | sporadic | 58104 | 49709 | 4666 | 3720 |
| answerals | CASE_NEUJK720JCL | als | sporadic | 63459 | 53214 | 6353 | 3879 |
| answerals | CASE_NEUJL547WVQ | als | sporadic | 66479 | 58462 | 3618 | 4387 |
| answerals | CASE_NEUJL595JAZ | als | sporadic | 68444 | 59292 | 4865 | 4278 |
| answerals | CASE_NEUJP935AVF | als | sporadic | 58826 | 50443 | 4557 | 3815 |
| answerals | CASE_NEUJX780XXK | als | sporadic | 58759 | 50213 | 4626 | 3913 |
| answerals | CASE_NEUJX990GR5 | als | c9orf72 | 62532 | 53432 | 5134 | 3957 |
| answerals | CASE_NEUJY426MBU | als | sporadic | 63184 | 53940 | 5247 | 3990 |
| answerals | CASE_NEUJY536DKF | als | sporadic | 58841 | 50172 | 4803 | 3859 |
| answerals | CASE_NEUKA860NUG | als | sporadic | 57475 | 49594 | 4413 | 3465 |
| answerals | CASE_NEUKD025JPF | als | sporadic | 53032 | 45368 | 4160 | 3495 |
| answerals | CASE_NEUKP160HX8 | als | sporadic | 60955 | 52292 | 4709 | 3940 |
| answerals | CASE_NEUKR376CW3 | als | sporadic | 59716 | 51083 | 4859 | 3767 |
| answerals | CASE_NEUKV547CFA | als | sporadic | 58332 | 50402 | 4378 | 3545 |
| answerals | CASE_NEUKY704JVA | als | sporadic | 57919 | 49881 | 4214 | 3817 |
| answerals | CASE_NEULA694DDC | als | sporadic | 56553 | 48081 | 4925 | 3538 |
| answerals | CASE_NEULA777DBT | als | sporadic | 60828 | 52252 | 4780 | 3788 |
| answerals | CASE_NEULD354RZB | als | sporadic | 58571 | 50309 | 4500 | 3756 |
| answerals | CASE_NEULH729AU2 | als | sporadic | 56790 | 48811 | 4431 | 3540 |
| answerals | CASE_NEULL588ALG | als | sporadic | 58040 | 50064 | 4307 | 3660 |
| answerals | CASE_NEULL648LJ1 | als | sporadic | 59952 | 51253 | 4757 | 3931 |
| answerals | CASE_NEULP998KDJ | als | sporadic | 55783 | 48072 | 3973 | 3727 |
| answerals | CASE_NEULT851ENP | als | sporadic | 57842 | 49090 | 4970 | 3777 |
| answerals | CASE_NEULY177TTN | als | sporadic | 54390 | 46686 | 4203 | 3497 |
| answerals | CASE_NEULY328CRJ | als | sporadic | 57720 | 49451 | 4533 | 3729 |
| answerals | CASE_NEULZ548ZXV | als | sporadic | 68624 | 59417 | 4897 | 4298 |
| answerals | CASE_NEUMB242CLN | als | sporadic | 64129 | 55161 | 5047 | 3916 |
| answerals | CASE_NEUME498PCJ | als | sporadic | 58309 | 50715 | 3999 | 3585 |
| answerals | CASE_NEUMH634MKT | als | sporadic | 60658 | 51952 | 4866 | 3832 |
| answerals | CASE_NEUMN012EVP | als | sporadic | 58561 | 50094 | 4680 | 3778 |
| answerals | CASE_NEUMW598YMT | als | sporadic | 62333 | 53419 | 5026 | 3878 |
| answerals | CASE_NEUMY871DGF | als | sporadic | 60697 | 51759 | 5020 | 3907 |
| answerals | CASE_NEUNA248WXL | als | sporadic | 55051 | 47376 | 4045 | 3621 |
| answerals | CASE_NEUNG326MFP | als | sporadic | 61248 | 52461 | 4840 | 3937 |
| answerals | CASE_NEUNJ155KYL | als | sporadic | 60514 | 51907 | 4617 | 3984 |
| answerals | CASE_NEUNJ938DUL | als | sporadic | 59969 | 51779 | 4561 | 3625 |
| answerals | CASE_NEUNL303HLF | als | sporadic | 56991 | 48903 | 4274 | 3802 |
| answerals | CASE_NEUNL415AFW | als | c9orf72 | 57236 | 49163 | 4505 | 3561 |
| answerals | CASE_NEUNR020KV6 | als | sporadic | 57657 | 49284 | 4569 | 3797 |
| answerals | CASE_NEUNZ171UYF | als | sporadic | 58352 | 49773 | 4750 | 3822 |
| answerals | CASE_NEUPG593UTV | als | sporadic | 60219 | 51623 | 4928 | 3658 |
| answerals | CASE_NEUPK546ZLD | als | c9orf72 | 58822 | 50244 | 4762 | 3809 |
| answerals | CASE_NEUPM937TMY | als | sporadic | 56356 | 48263 | 4429 | 3656 |
| answerals | CASE_NEUPN525XEW | als | sporadic | 56269 | 48342 | 4398 | 3523 |
| answerals | CASE_NEUPR357AUF | als | sporadic | 60436 | 51732 | 4868 | 3825 |
| answerals | CASE_NEUPR600MBU | als | sporadic | 55080 | 47217 | 4373 | 3486 |
| answerals | CASE_NEUPY050ANK | als | sporadic | 59160 | 50401 | 5042 | 3705 |
| answerals | CASE_NEURA639MK8 | als | sporadic | 53531 | 46259 | 3799 | 3464 |
| answerals | CASE_NEURF720KHA | als | sporadic | 57317 | 49163 | 4440 | 3708 |
| answerals | CASE_NEURJ362MXH | als | setx | 57101 | 49137 | 4246 | 3708 |
| answerals | CASE_NEURR881FKY | als | sporadic | 56549 | 48837 | 4135 | 3570 |
| answerals | CASE_NEURX315DYH | als | sporadic | 57026 | 48201 | 5162 | 3652 |
| answerals | CASE_NEURX909UL6 | als | sporadic | 57249 | 48874 | 4767 | 3599 |
| answerals | CASE_NEUTA057AF6 | als | sod1 | 63145 | 54036 | 5095 | 3999 |
| answerals | CASE_NEUTA689LN5 | als | sporadic | 57830 | 49621 | 4555 | 3644 |
| answerals | CASE_NEUTB230DA3 | als | sporadic | 68334 | 58838 | 5088 | 4393 |
| answerals | CASE_NEUTC791PVE | als | sporadic | 64212 | 55029 | 5293 | 3881 |
| answerals | CASE_NEUTD314VFT | als | sporadic | 58647 | 50159 | 4656 | 3823 |
| answerals | CASE_NEUTD713DE3 | als | sporadic | 56983 | 48958 | 4482 | 3534 |
| answerals | CASE_NEUTD866EAH | als | sporadic | 70740 | 60910 | 5440 | 4375 |
| answerals | CASE_NEUTJ613AH9 | als | sporadic | 53539 | 45913 | 4221 | 3399 |
| answerals | CASE_NEUTL257PNR | als | sporadic | 57838 | 49524 | 4614 | 3687 |
| answerals | CASE_NEUTL699WJ0 | als | sporadic | 60387 | 51630 | 4950 | 3799 |
| answerals | CASE_NEUTM934BPY | als | sporadic | 60947 | 51341 | 5935 | 3661 |
| answerals | CASE_NEUTN952DDG | als | c9orf72 | 56066 | 48151 | 4328 | 3580 |
| answerals | CASE_NEUTU360YJY | als | sporadic | 59112 | 50447 | 4749 | 3908 |
| answerals | CASE_NEUUC458RFT | als | c9orf72 | 61553 | 53233 | 4547 | 3765 |
| answerals | CASE_NEUUD158CJF | als | sporadic | 59508 | 50942 | 4824 | 3730 |
| answerals | CASE_NEUUE852BB1 | als | sporadic | 56400 | 48072 | 4698 | 3619 |
| answerals | CASE_NEUUF613PHL | als | sporadic | 55668 | 47492 | 4621 | 3545 |
| answerals | CASE_NEUUH658EYH | als | sporadic | 67044 | 57942 | 4822 | 4271 |
| answerals | CASE_NEUUJ507EAB | als | sporadic | 58926 | 51621 | 3506 | 3788 |
| answerals | CASE_NEUUL256UC9 | als | c9orf72 | 58166 | 50041 | 4368 | 3743 |
| answerals | CASE_NEUUL292XRC | als | sporadic | 59515 | 51097 | 4721 | 3686 |
| answerals | CASE_NEUUL311NRQ | als | sporadic | 57975 | 49431 | 4783 | 3749 |
| answerals | CASE_NEUUP280KXL | als | sporadic | 58169 | 49874 | 4518 | 3770 |
| answerals | CASE_NEUUU506WZF | als | sporadic | 59501 | 50857 | 4906 | 3733 |
| answerals | CASE_NEUUZ216XY8 | als | sporadic | 61825 | 52520 | 5471 | 3828 |
| answerals | CASE_NEUVD687XD8 | als | sporadic | 63026 | 54907 | 4313 | 3796 |
| answerals | CASE_NEUVF888UHM | als | sporadic | 54658 | 47080 | 4082 | 3494 |
| answerals | CASE_NEUVJ560JGZ | als | sporadic | 60403 | 51758 | 4810 | 3826 |
| answerals | CASE_NEUVM674HUA | als | sporadic | 56991 | 49038 | 4448 | 3496 |
| answerals | CASE_NEUVN746WKV | als | sporadic | 58209 | 50322 | 4279 | 3598 |
| answerals | CASE_NEUVP060WFG | als | sporadic | 58717 | 50229 | 4679 | 3797 |
| answerals | CASE_NEUVR636VTP | als | sporadic | 59011 | 50635 | 4539 | 3834 |
| answerals | CASE_NEUVR814YCY | als | sporadic | 60715 | 52433 | 4462 | 3810 |
| answerals | CASE_NEUVU735HU6 | als | sporadic | 69147 | 60054 | 4847 | 4231 |
| answerals | CASE_NEUVV225XKB | als | sporadic | 59317 | 50646 | 4759 | 3901 |
| answerals | CASE_NEUVW680LPK | als | c9orf72 | 57874 | 49510 | 4588 | 3767 |
| answerals | CASE_NEUVW999FP9 | als | sporadic | 59423 | 51099 | 4516 | 3797 |
| answerals | CASE_NEUVX902YNL | als | c9orf72 | 54908 | 46768 | 4417 | 3720 |
| answerals | CASE_NEUWD538KT3 | als | c9orf72 | 56245 | 48044 | 4604 | 3589 |
| answerals | CASE_NEUWD946RDA | als | sporadic | 62506 | 53415 | 5157 | 3926 |
| answerals | CASE_NEUWH380YHV | als | sporadic | 59186 | 50751 | 4635 | 3790 |
| answerals | CASE_NEUWH955FJF | als | sporadic | 61047 | 52562 | 4604 | 3873 |
| answerals | CASE_NEUWJ389FC7 | als | sporadic | 57396 | 49162 | 4466 | 3759 |
| answerals | CASE_NEUWM344ZLM | als | sod1 | 55629 | 47637 | 4284 | 3703 |
| answerals | CASE_NEUWP426NBR | als | sporadic | 57165 | 49264 | 4286 | 3605 |
| answerals | CASE_NEUWX167DAH | als | sporadic | 58440 | 50098 | 4519 | 3815 |
| answerals | CASE_NEUWY079WUH | als | sporadic | 66375 | 56843 | 5286 | 4234 |
| answerals | CASE_NEUWZ614ARQ | als | sporadic | 54933 | 46815 | 4446 | 3664 |
| answerals | CASE_NEUXD985ZU1 | als | sporadic | 59705 | 51105 | 4765 | 3824 |
| answerals | CASE_NEUXE491RMM | als | sporadic | 55908 | 48343 | 3994 | 3565 |
| answerals | CASE_NEUXG265ME9 | als | sporadic | 58728 | 50395 | 4414 | 3905 |
| answerals | CASE_NEUXH833LL4 | als | sporadic | 59041 | 50605 | 4621 | 3805 |
| answerals | CASE_NEUXP289KRC | als | sod1 | 57123 | 48766 | 4667 | 3684 |
| answerals | CASE_NEUXP495XE2 | als | sporadic | 59608 | 51399 | 4358 | 3842 |
| answerals | CASE_NEUXP595FFP | als | sporadic | 53531 | 45773 | 4199 | 3551 |
| answerals | CASE_NEUXV122FN3 | als | sporadic | 61048 | 52398 | 4683 | 3955 |
| answerals | CASE_NEUXX361RUG | als | sporadic | 55793 | 48069 | 4188 | 3530 |
| answerals | CASE_NEUYC055XPZ | als | sporadic | 57919 | 49334 | 4796 | 3776 |
| answerals | CASE_NEUYC303AJY | als | sporadic | 58961 | 50283 | 4820 | 3846 |
| answerals | CASE_NEUYD306HAB | als | sporadic | 58116 | 49543 | 5005 | 3556 |
| answerals | CASE_NEUYG208KVV | als | sporadic | 56507 | 48381 | 4375 | 3744 |
| answerals | CASE_NEUYG298CA9 | als | sporadic | 60406 | 51438 | 5148 | 3813 |
| answerals | CASE_NEUYH924UCE | als | sporadic | 60296 | 51515 | 4748 | 4023 |
| answerals | CASE_NEUYJ705VN9 | als | sporadic | 60720 | 52113 | 4782 | 3815 |
| answerals | CASE_NEUYK029WUU | als | sporadic | 55198 | 47101 | 4462 | 3624 |
| answerals | CASE_NEUYL008GM4 | als | sporadic | 57699 | 49865 | 4109 | 3717 |
| answerals | CASE_NEUYL149PRF | als | sporadic | 56637 | 48855 | 4120 | 3655 |
| answerals | CASE_NEUYP226CPW | als | sporadic | 61950 | 53333 | 4720 | 3886 |
| answerals | CASE_NEUYP235ZLD | als | tardbp | 56820 | 48881 | 4254 | 3675 |
| answerals | CASE_NEUYT193FFG | als | sporadic | 58074 | 49545 | 4676 | 3843 |
| answerals | CASE_NEUYY225MNZ | als | c9orf72 | 53495 | 46046 | 3923 | 3522 |
| answerals | CASE_NEUYY614DN8 | als | sporadic | 62481 | 53489 | 5170 | 3811 |
| answerals | CASE_NEUYY878JGP | als | sporadic | 60999 | 52371 | 4890 | 3730 |
| answerals | CASE_NEUZD231YZ6 | als | sporadic | 54797 | 46712 | 4520 | 3555 |
| answerals | CASE_NEUZE432DZM | als | sporadic | 61125 | 52221 | 5070 | 3824 |
| answerals | CASE_NEUZF321EW4 | als | sod1 | 57596 | 49433 | 4445 | 3714 |
| answerals | CASE_NEUZF473UEP | als | sporadic | 64617 | 55405 | 5175 | 4030 |
| answerals | CASE_NEUZJ053JGZ | als | sporadic | 59197 | 50800 | 4539 | 3853 |
| answerals | CASE_NEUZK054DP5 | als | sporadic | 58652 | 50511 | 4362 | 3769 |
| answerals | CASE_NEUZN836GME | als | sporadic | 60499 | 51754 | 4899 | 3836 |
| answerals | CASE_NEUZN936HJ9 | als | sporadic | 55162 | 47141 | 4250 | 3767 |
| answerals | CASE_NEUZP278MR4 | als | sporadic | 58249 | 49800 | 4552 | 3889 |
| answerals | CASE_NEUZT557DHF | als | sporadic | 59667 | 51310 | 4558 | 3792 |
| answerals | CASE_NEUZT902WVB | als | sporadic | 63471 | 54337 | 4965 | 4155 |
| answerals | CASE_NEUZV656DD1 | als | sporadic | 69727 | 60051 | 5192 | 4473 |
| answerals | CASE_NEUZW701NNF | als | c9orf72 | 54607 | 46701 | 4364 | 3535 |
| answerals | CASE_NEUZX521TKK | als | sporadic | 56578 | 48274 | 4694 | 3604 |
| answerals | CASE_NEUZX847VWV | als | sporadic | 58281 | 49775 | 4672 | 3831 |
| answerals | CASE_NEUZY128BJ2 | als | sporadic | 63551 | 54316 | 5192 | 4036 |
| answerals | CASE_NEUZY975XKL | als | sporadic | 57443 | 49428 | 4230 | 3778 |
| answerals | CTRL_NEUAA485DZL | ctrl | ctrl | 63238 | 54544 | 4780 | 3909 |
| answerals | CTRL_NEUAJ025JC3 | ctrl | ctrl | 56132 | 48574 | 4080 | 3466 |
| answerals | CTRL_NEUAJ928PAA | ctrl | ctrl | 58615 | 50164 | 4733 | 3710 |
| answerals | CTRL_NEUCA748GF2 | ctrl | ctrl | 57039 | 48969 | 4365 | 3699 |
| answerals | CTRL_NEUCV136DHM | ctrl | ctrl | 60751 | 51891 | 4924 | 3924 |
| answerals | CTRL_NEUCV809LL4 | ctrl | ctrl | 53289 | 45860 | 4098 | 3323 |
| answerals | CTRL_NEUDA782GW3 | ctrl | ctrl | 57198 | 49513 | 4260 | 3415 |
| answerals | CTRL_NEUDE949BP3 | ctrl | ctrl | 57359 | 49426 | 4398 | 3529 |
| answerals | CTRL_NEUDM126GNG | ctrl | ctrl | 59261 | 50526 | 4954 | 3766 |
| answerals | CTRL_NEUDT762KUL | ctrl | ctrl | 55473 | 47767 | 4227 | 3468 |
| answerals | CTRL_NEUEB210XRC | ctrl | ctrl | 57704 | 49296 | 4689 | 3707 |
| answerals | CTRL_NEUEY565NWT | ctrl | ctrl | 56602 | 48391 | 4712 | 3489 |
| answerals | CTRL_NEUFL733GX5 | ctrl | ctrl | 64451 | 54811 | 5716 | 3914 |
| answerals | CTRL_NEUFZ500KDB | ctrl | ctrl | 57073 | 48888 | 4595 | 3581 |
| answerals | CTRL_NEUFZ508VBV | ctrl | ctrl | 53898 | 46830 | 3735 | 3326 |
| answerals | CTRL_NEUHE723FGT | ctrl | ctrl | 58113 | 50153 | 4255 | 3694 |
| answerals | CTRL_NEUHZ716BZ2 | ctrl | ctrl | 54109 | 46540 | 4156 | 3404 |
| answerals | CTRL_NEUJH290RH7 | ctrl | ctrl | 53571 | 46469 | 3731 | 3367 |
| answerals | CTRL_NEUJX341NDP | ctrl | ctrl | 53093 | 45615 | 4041 | 3427 |
| answerals | CTRL_NEUKW131XJ2 | ctrl | ctrl | 55174 | 47339 | 4338 | 3490 |
| answerals | CTRL_NEULL933JXY | ctrl | ctrl | 57664 | 49898 | 4032 | 3723 |
| answerals | CTRL_NEUMA002VLD | ctrl | ctrl | 59949 | 51244 | 4686 | 4011 |
| answerals | CTRL_NEUMF089KLV | ctrl | ctrl | 56930 | 48697 | 4475 | 3751 |
| answerals | CTRL_NEUML507PFJ | ctrl | ctrl | 55269 | 47121 | 4524 | 3616 |
| answerals | CTRL_NEUMN061ATZ | ctrl | ctrl | 53189 | 45465 | 4159 | 3552 |
| answerals | CTRL_NEUMT184NWC | ctrl | ctrl | 60108 | 51580 | 4731 | 3791 |
| answerals | CTRL_NEUNC876ZB2 | ctrl | ctrl | 61491 | 52926 | 4499 | 4057 |
| answerals | CTRL_NEUNN472ACB | ctrl | ctrl | 69191 | 59326 | 5702 | 4149 |
| answerals | CTRL_NEUNW343RXP | ctrl | ctrl | 55652 | 47504 | 4485 | 3657 |
| answerals | CTRL_NEUPH301NNX | ctrl | ctrl | 54521 | 47158 | 3958 | 3397 |
| answerals | CTRL_NEUPL878MTL | ctrl | ctrl | 58345 | 50015 | 4518 | 3804 |
| answerals | CTRL_NEUPW536ZKZ | ctrl | ctrl | 58923 | 50330 | 4811 | 3771 |
| answerals | CTRL_NEURJ861MMD | ctrl | ctrl | 58755 | 51011 | 4136 | 3605 |
| answerals | CTRL_NEURV546WMW | ctrl | ctrl | 61817 | 53187 | 4606 | 4015 |
| answerals | CTRL_NEUUV825HYF | ctrl | ctrl | 54032 | 46512 | 4121 | 3389 |
| answerals | CTRL_NEUVZ050YX7 | ctrl | ctrl | 54408 | 46947 | 4018 | 3437 |
| answerals | CTRL_NEUWN092BVG | ctrl | ctrl | 56657 | 48926 | 3971 | 3752 |
| answerals | CTRL_NEUWT164JRQ | ctrl | ctrl | 58778 | 50113 | 4861 | 3794 |
| answerals | CTRL_NEUXC258VTR | ctrl | ctrl | 61355 | 52769 | 4716 | 3859 |
| answerals | CTRL_NEUXP955XW7 | ctrl | ctrl | 58954 | 50522 | 4798 | 3628 |
| answerals | CTRL_NEUXW311EFC | ctrl | ctrl | 53050 | 45720 | 3940 | 3384 |
| answerals | CTRL_NEUYM205MRL | ctrl | ctrl | 58659 | 50854 | 4064 | 3734 |
ipsc_mn_als_datasets.starfusion.n = ipsc_mn_als_datasets.starfusion %>%
add_count(dataset_sample) %>% # count number of fusions per sample
distinct(dataset_sample, .keep_all = TRUE) %>% select(dataset, sample, condition, fusion_number = n, total_reads, dataset_sample, mutation) #keep 1 row per sample
# add samples with 0 fusions
ipsc_mn_als_datasets.starfusion.samples_no_fusions = ipsc_mn_als_datasets.paired_end.metadata$dataset_sample[!ipsc_mn_als_datasets.paired_end.metadata$dataset_sample %in% ipsc_mn_als_datasets.starfusion.n$dataset_sample]
ipsc_mn_als_datasets.paired_end.metadata.no_fusions = ipsc_mn_als_datasets.paired_end.metadata %>% filter(dataset_sample %in% ipsc_mn_als_datasets.starfusion.samples_no_fusions) %>%
left_join(multiqc_rseqc_read_distribution.tsv) %>%
mutate(fusion_number = 0) %>% select(dataset_sample, sample, fusion_number, condition, dataset, total_reads, mutation)
ipsc_mn_als_datasets.starfusion.n = bind_rows(ipsc_mn_als_datasets.starfusion.n, ipsc_mn_als_datasets.paired_end.metadata.no_fusions)
ipsc_mn_als_datasets.starfusion.table_s9 = ipsc_mn_als_datasets.starfusion.n %>% select(dataset, sample, condition, mutation, fusion_number, total_reads)
kbl(ipsc_mn_als_datasets.starfusion.table_s9) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), fixed_thead = T) %>% scroll_box(width = "100%", height = "500px")| dataset | sample | condition | mutation | fusion_number | total_reads |
|---|---|---|---|---|---|
| answerals | CASE_NEUDE902GCT | als | c9orf72 | 13 | 80351595 |
| answerals | CTRL_NEUAA485DZL | ctrl | ctrl | 6 | 92629631 |
| answerals | CASE_NEUAA599TMX | als | sporadic | 6 | 77223828 |
| answerals | CASE_NEUAB000NKC | als | c9orf72 | 31 | 71106777 |
| answerals | CASE_NEUAE228FF6 | als | sporadic | 2 | 63533855 |
| answerals | CASE_NEUAE993EPR | als | sporadic | 9 | 93223837 |
| answerals | CASE_NEUAF553MJ3 | als | sporadic | 8 | 92294028 |
| answerals | CASE_NEUAG241NUD | als | sporadic | 7 | 88487027 |
| answerals | CASE_NEUAG603XLK | als | pfn1 | 11 | 41359233 |
| answerals | CASE_NEUAG766ULB | als | sporadic | 12 | 85338776 |
| answerals | CTRL_NEUAJ025JC3 | ctrl | ctrl | 15 | 78856459 |
| answerals | CTRL_NEUAJ928PAA | ctrl | ctrl | 16 | 96697354 |
| answerals | CASE_NEUAL076FCE | als | sporadic | 12 | 88517839 |
| answerals | CASE_NEUAM655HF7 | als | sporadic | 12 | 70099172 |
| answerals | CASE_NEUAP285GGU | als | sporadic | 15 | 71653943 |
| answerals | CASE_NEUAT234RK6 | als | sporadic | 14 | 86690836 |
| answerals | CASE_NEUAW157NMJ | als | sporadic | 25 | 94641466 |
| answerals | CASE_NEUAW717TN6 | als | sporadic | 8 | 96444518 |
| answerals | CASE_NEUAX665ZHY | als | sporadic | 11 | 96375698 |
| answerals | CASE_NEUAY067UTB | als | chchd1 | 14 | 103940017 |
| answerals | CASE_NEUAZ394JEZ | als | sporadic | 7 | 90298769 |
| answerals | CASE_NEUBA169GXD | als | sporadic | 13 | 90044591 |
| answerals | CASE_NEUBC901KL3 | als | sporadic | 11 | 96083124 |
| answerals | CASE_NEUBC998WWB | als | sqstm1 | 11 | 97383223 |
| answerals | CASE_NEUBD218YR3 | als | fig4 | 19 | 72915834 |
| answerals | CASE_NEUBD288RXQ | als | sporadic | 10 | 92088313 |
| answerals | CASE_NEUBK117YXL | als | sporadic | 21 | 92338200 |
| answerals | CASE_NEUBM949LA5 | als | sporadic | 9 | 86250060 |
| answerals | CASE_NEUBN979ZZ5 | als | sporadic | 4 | 89827770 |
| answerals | CASE_NEUBT273FH3 | als | sporadic | 17 | 74542618 |
| answerals | CASE_NEUBW008RJ5 | als | sporadic | 14 | 106645947 |
| answerals | CASE_NEUBY734PFR | als | sporadic | 6 | 74456844 |
| answerals | CTRL_NEUCA748GF2 | ctrl | ctrl | 8 | 82008988 |
| answerals | CASE_NEUCB613CA9 | als | sporadic | 9 | 90541534 |
| answerals | CASE_NEUCD502BFU | als | sod1 | 9 | 89586112 |
| answerals | CASE_NEUCE965ZGK | als | c9orf72 | 20 | 78627760 |
| answerals | CASE_NEUCF538BRM | als | sporadic | 7 | 97574144 |
| answerals | CASE_NEUCG511MJ6 | als | sporadic | 6 | 98813421 |
| answerals | CASE_NEUCN596RR3 | als | sporadic | 5 | 89512093 |
| answerals | CASE_NEUCP218XVV | als | sporadic | 12 | 93789222 |
| answerals | CASE_NEUCT022VTK | als | sporadic | 11 | 100874817 |
| answerals | CASE_NEUCT842RJV | als | sod1 | 26 | 86138539 |
| answerals | CASE_NEUCU076ADN | als | sporadic | 6 | 95677719 |
| answerals | CASE_NEUCU245GBQ | als | sporadic | 12 | 72116830 |
| answerals | CTRL_NEUCV136DHM | ctrl | ctrl | 10 | 96543719 |
| answerals | CASE_NEUCV578DFJ | als | sporadic | 10 | 72026572 |
| answerals | CTRL_NEUCV809LL4 | ctrl | ctrl | 19 | 60185905 |
| answerals | CTRL_NEUDA782GW3 | ctrl | ctrl | 16 | 71137627 |
| answerals | CASE_NEUDD018KAH | als | sporadic | 14 | 70760037 |
| answerals | CTRL_NEUDE949BP3 | ctrl | ctrl | 18 | 84067732 |
| answerals | CASE_NEUDG000ZG5 | als | sporadic | 13 | 79910862 |
| answerals | CASE_NEUDG272XWC | als | sporadic | 10 | 82329332 |
| answerals | CASE_NEUDH063DEA | als | sporadic | 8 | 66730587 |
| answerals | CTRL_NEUDM126GNG | ctrl | ctrl | 12 | 89281476 |
| answerals | CASE_NEUDM949BAR | als | sporadic | 9 | 79446358 |
| answerals | CASE_NEUDP155HFH | als | sporadic | 8 | 104761280 |
| answerals | CASE_NEUDT709YHN | als | c9orf72 | 6 | 80752554 |
| answerals | CTRL_NEUDT762KUL | ctrl | ctrl | 17 | 68969167 |
| answerals | CASE_NEUDY534KGP | als | sporadic | 10 | 91012561 |
| answerals | CASE_NEUDZ473EGM | als | c9orf72 | 10 | 112302126 |
| answerals | CTRL_NEUEB210XRC | ctrl | ctrl | 10 | 83801109 |
| answerals | CASE_NEUEB422WW0 | als | sporadic | 18 | 102960267 |
| answerals | CASE_NEUEC400NYR | als | setx | 7 | 92373132 |
| answerals | CASE_NEUEK191WYC | als | sporadic | 9 | 84425639 |
| answerals | CASE_NEUEM029XXZ | als | sporadic | 14 | 77394197 |
| answerals | CASE_NEUEM720BUU | als | c9orf72 | 39 | 63755467 |
| answerals | CASE_NEUEN017PCJ | als | sporadic | 10 | 90774153 |
| answerals | CASE_NEUEN476CLW | als | c9orf72 | 21 | 76588865 |
| answerals | CASE_NEUET072VDG | als | sporadic | 15 | 95322550 |
| answerals | CASE_NEUEU318NY2 | als | sporadic | 13 | 91271120 |
| answerals | CASE_NEUEU558MNK | als | sporadic | 13 | 83207564 |
| answerals | CASE_NEUEY478NZP | als | sod1 | 13 | 83363466 |
| answerals | CTRL_NEUEY565NWT | ctrl | ctrl | 10 | 82690328 |
| answerals | CASE_NEUFB989DT1 | als | sporadic | 6 | 80810272 |
| answerals | CASE_NEUFH122WN7 | als | sqstm1 | 5 | 108588802 |
| answerals | CASE_NEUFH461AAN | als | sporadic | 20 | 95778777 |
| answerals | CTRL_NEUFL733GX5 | ctrl | ctrl | 6 | 94018469 |
| answerals | CASE_NEUFU395MJD | als | sporadic | 11 | 72993028 |
| answerals | CASE_NEUFV237VCZ | als | c9orf72 | 20 | 89352295 |
| answerals | CASE_NEUFX386KMB | als | sporadic | 9 | 96918010 |
| answerals | CASE_NEUFY342UNG | als | sporadic | 10 | 90963548 |
| answerals | CTRL_NEUFZ500KDB | ctrl | ctrl | 11 | 85044761 |
| answerals | CTRL_NEUFZ508VBV | ctrl | ctrl | 8 | 75909259 |
| answerals | CASE_NEUGD965XVD | als | sporadic | 5 | 103651614 |
| answerals | CASE_NEUGE540TC4 | als | sporadic | 11 | 64036466 |
| answerals | CASE_NEUGH995TFK | als | c9orf72 | 7 | 85349248 |
| answerals | CASE_NEUGJ081HKR | als | c9orf72 | 8 | 75455646 |
| answerals | CASE_NEUGL543NJ1 | als | sporadic | 9 | 92931442 |
| answerals | CASE_NEUGP781PDU | als | sporadic | 10 | 80833254 |
| answerals | CASE_NEUGR121TFD | als | sporadic | 15 | 102872584 |
| answerals | CASE_NEUGR539MVT | als | sporadic | 7 | 94175062 |
| answerals | CASE_NEUGW326BRV | als | sporadic | 18 | 69987454 |
| answerals | CASE_NEUGW340YEB | als | sporadic | 15 | 98422534 |
| answerals | CASE_NEUHB491NGF | als | sporadic | 12 | 105880561 |
| answerals | CTRL_NEUHE723FGT | ctrl | ctrl | 13 | 98431529 |
| answerals | CASE_NEUHG644RYB | als | sporadic | 9 | 96700132 |
| answerals | CASE_NEUHG791RV5 | als | sporadic | 15 | 93752450 |
| answerals | CASE_NEUHK991AVP | als | sod1 | 12 | 95449413 |
| answerals | CASE_NEUHL999WWT | als | sporadic | 11 | 91645541 |
| answerals | CASE_NEUHM532NDD | als | sporadic | 12 | 97995986 |
| answerals | CASE_NEUHT569HT1 | als | sporadic | 7 | 97925023 |
| answerals | CASE_NEUHV216EHA | als | sporadic | 10 | 100671641 |
| answerals | CASE_NEUHW530WD8 | als | sporadic | 16 | 105977870 |
| answerals | CASE_NEUHW590KBH | als | sporadic | 10 | 72181419 |
| answerals | CASE_NEUHY206ZEQ | als | sporadic | 18 | 74090361 |
| answerals | CASE_NEUHZ302VU4 | als | sporadic | 13 | 67530789 |
| answerals | CTRL_NEUHZ716BZ2 | ctrl | ctrl | 13 | 71207355 |
| answerals | CASE_NEUJA217MTJ | als | sporadic | 6 | 115185396 |
| answerals | CASE_NEUJA666PYD | als | sporadic | 19 | 80935095 |
| answerals | CASE_NEUJC191RLE | als | pfn1 | 8 | 101473499 |
| answerals | CASE_NEUJG311WGV | als | sporadic | 10 | 90925131 |
| answerals | CASE_NEUJG885PY7 | als | sporadic | 13 | 98116859 |
| answerals | CASE_NEUJH197AK2 | als | sporadic | 20 | 77814469 |
| answerals | CTRL_NEUJH290RH7 | ctrl | ctrl | 6 | 66856215 |
| answerals | CASE_NEUJK720JCL | als | sporadic | 6 | 106522739 |
| answerals | CASE_NEUJL547WVQ | als | sporadic | 7 | 86686484 |
| answerals | CASE_NEUJL595JAZ | als | sporadic | 16 | 85731672 |
| answerals | CASE_NEUJP935AVF | als | sporadic | 7 | 88750101 |
| answerals | CTRL_NEUJX341NDP | ctrl | ctrl | 7 | 71651755 |
| answerals | CASE_NEUJX780XXK | als | sporadic | 5 | 100118041 |
| answerals | CASE_NEUJX990GR5 | als | c9orf72 | 2 | 112621195 |
| answerals | CASE_NEUJY426MBU | als | sporadic | 6 | 122500065 |
| answerals | CASE_NEUJY536DKF | als | sporadic | 10 | 98537826 |
| answerals | CASE_NEUKA860NUG | als | sporadic | 15 | 62840884 |
| answerals | CASE_NEUKD025JPF | als | sporadic | 12 | 60919280 |
| answerals | CASE_NEUKP160HX8 | als | sporadic | 12 | 102003991 |
| answerals | CASE_NEUKR376CW3 | als | sporadic | 12 | 97538990 |
| answerals | CASE_NEUKV547CFA | als | sporadic | 12 | 69364009 |
| answerals | CTRL_NEUKW131XJ2 | ctrl | ctrl | 17 | 74096752 |
| answerals | CASE_NEUKY704JVA | als | sporadic | 9 | 80410172 |
| answerals | CASE_NEULA694DDC | als | sporadic | 10 | 72567703 |
| answerals | CASE_NEULA777DBT | als | sporadic | 18 | 110522400 |
| answerals | CASE_NEULD354RZB | als | sporadic | 12 | 92499799 |
| answerals | CASE_NEULH729AU2 | als | sporadic | 8 | 66477122 |
| answerals | CASE_NEULL588ALG | als | sporadic | 7 | 83847300 |
| answerals | CASE_NEULL648LJ1 | als | sporadic | 14 | 110155878 |
| answerals | CTRL_NEULL933JXY | ctrl | ctrl | 7 | 82671867 |
| answerals | CASE_NEULP998KDJ | als | sporadic | 8 | 77194450 |
| answerals | CASE_NEULT851ENP | als | sporadic | 7 | 99055975 |
| answerals | CASE_NEULY177TTN | als | sporadic | 17 | 67915998 |
| answerals | CASE_NEULY328CRJ | als | sporadic | 13 | 84555017 |
| answerals | CASE_NEULZ548ZXV | als | sporadic | 20 | 83302460 |
| answerals | CTRL_NEUMA002VLD | ctrl | ctrl | 6 | 93511645 |
| answerals | CASE_NEUMB242CLN | als | sporadic | 14 | 104455218 |
| answerals | CASE_NEUME498PCJ | als | sporadic | 7 | 93041938 |
| answerals | CTRL_NEUMF089KLV | ctrl | ctrl | 7 | 77138477 |
| answerals | CASE_NEUMH634MKT | als | sporadic | 12 | 101656984 |
| answerals | CTRL_NEUML507PFJ | ctrl | ctrl | 8 | 68142265 |
| answerals | CASE_NEUMN012EVP | als | sporadic | 8 | 95638539 |
| answerals | CTRL_NEUMN061ATZ | ctrl | ctrl | 12 | 77105679 |
| answerals | CTRL_NEUMT184NWC | ctrl | ctrl | 12 | 92838742 |
| answerals | CASE_NEUMW598YMT | als | sporadic | 10 | 100036715 |
| answerals | CASE_NEUMY871DGF | als | sporadic | 5 | 109363694 |
| answerals | CASE_NEUNA248WXL | als | sporadic | 7 | 73992295 |
| answerals | CTRL_NEUNC876ZB2 | ctrl | ctrl | 6 | 83265656 |
| answerals | CASE_NEUNG326MFP | als | sporadic | 7 | 100565728 |
| answerals | CASE_NEUNJ155KYL | als | sporadic | 7 | 95718335 |
| answerals | CASE_NEUNJ938DUL | als | sporadic | 11 | 75727499 |
| answerals | CASE_NEUNL303HLF | als | sporadic | 12 | 77783363 |
| answerals | CASE_NEUNL415AFW | als | c9orf72 | 23 | 72450848 |
| answerals | CTRL_NEUNN472ACB | ctrl | ctrl | 15 | 78003255 |
| answerals | CASE_NEUNR020KV6 | als | sporadic | 5 | 79298369 |
| answerals | CTRL_NEUNW343RXP | ctrl | ctrl | 9 | 67553681 |
| answerals | CASE_NEUNZ171UYF | als | sporadic | 5 | 113844202 |
| answerals | CASE_NEUPG593UTV | als | sporadic | 14 | 81542271 |
| answerals | CTRL_NEUPH301NNX | ctrl | ctrl | 12 | 81219399 |
| answerals | CASE_NEUPK546ZLD | als | c9orf72 | 16 | 95071196 |
| answerals | CTRL_NEUPL878MTL | ctrl | ctrl | 10 | 88824097 |
| answerals | CASE_NEUPM937TMY | als | sporadic | 16 | 78296968 |
| answerals | CASE_NEUPN525XEW | als | sporadic | 29 | 77106625 |
| answerals | CASE_NEUPR357AUF | als | sporadic | 14 | 99795776 |
| answerals | CASE_NEUPR600MBU | als | sporadic | 12 | 78140048 |
| answerals | CTRL_NEUPW536ZKZ | ctrl | ctrl | 12 | 90333508 |
| answerals | CASE_NEUPY050ANK | als | sporadic | 9 | 85546543 |
| answerals | CASE_NEURA639MK8 | als | sporadic | 17 | 65451477 |
| answerals | CASE_NEURF720KHA | als | sporadic | 13 | 84067184 |
| answerals | CASE_NEURJ362MXH | als | setx | 6 | 93645424 |
| answerals | CTRL_NEURJ861MMD | ctrl | ctrl | 10 | 100766856 |
| answerals | CASE_NEURR881FKY | als | sporadic | 12 | 86886855 |
| answerals | CTRL_NEURV546WMW | ctrl | ctrl | 13 | 111102498 |
| answerals | CASE_NEURX315DYH | als | sporadic | 10 | 73562711 |
| answerals | CASE_NEURX909UL6 | als | sporadic | 19 | 79097478 |
| answerals | CASE_NEUTA057AF6 | als | sod1 | 12 | 108681404 |
| answerals | CASE_NEUTA689LN5 | als | sporadic | 19 | 78200437 |
| answerals | CASE_NEUTB230DA3 | als | sporadic | 13 | 89915287 |
| answerals | CASE_NEUTC791PVE | als | sporadic | 14 | 97793523 |
| answerals | CASE_NEUTD314VFT | als | sporadic | 9 | 85036873 |
| answerals | CASE_NEUTD713DE3 | als | sporadic | 19 | 86563683 |
| answerals | CASE_NEUTD866EAH | als | sporadic | 6 | 83462831 |
| answerals | CASE_NEUTJ613AH9 | als | sporadic | 6 | 60785280 |
| answerals | CASE_NEUTL257PNR | als | sporadic | 11 | 92252300 |
| answerals | CASE_NEUTL699WJ0 | als | sporadic | 8 | 84089003 |
| answerals | CASE_NEUTM934BPY | als | sporadic | 5 | 95659466 |
| answerals | CASE_NEUTN952DDG | als | c9orf72 | 25 | 81390541 |
| answerals | CASE_NEUTU360YJY | als | sporadic | 21 | 86008260 |
| answerals | CASE_NEUUC458RFT | als | c9orf72 | 7 | 85257121 |
| answerals | CASE_NEUUD158CJF | als | sporadic | 4 | 73223524 |
| answerals | CASE_NEUUE852BB1 | als | sporadic | 17 | 69679811 |
| answerals | CASE_NEUUF613PHL | als | sporadic | 9 | 88686748 |
| answerals | CASE_NEUUH658EYH | als | sporadic | 13 | 79107840 |
| answerals | CASE_NEUUJ507EAB | als | sporadic | 5 | 80476943 |
| answerals | CASE_NEUUL256UC9 | als | c9orf72 | 10 | 91609649 |
| answerals | CASE_NEUUL292XRC | als | sporadic | 10 | 72128909 |
| answerals | CASE_NEUUL311NRQ | als | sporadic | 9 | 100591313 |
| answerals | CASE_NEUUP280KXL | als | sporadic | 9 | 88847741 |
| answerals | CASE_NEUUU506WZF | als | sporadic | 3 | 91100217 |
| answerals | CTRL_NEUUV825HYF | ctrl | ctrl | 9 | 70624857 |
| answerals | CASE_NEUUZ216XY8 | als | sporadic | 12 | 84742547 |
| answerals | CASE_NEUVD687XD8 | als | sporadic | 13 | 85203015 |
| answerals | CASE_NEUVF888UHM | als | sporadic | 22 | 70783470 |
| answerals | CASE_NEUVJ560JGZ | als | sporadic | 8 | 115247071 |
| answerals | CASE_NEUVM674HUA | als | sporadic | 36 | 82820866 |
| answerals | CASE_NEUVN746WKV | als | sporadic | 27 | 84953195 |
| answerals | CASE_NEUVP060WFG | als | sporadic | 9 | 96612825 |
| answerals | CASE_NEUVR636VTP | als | sporadic | 15 | 95352910 |
| answerals | CASE_NEUVR814YCY | als | sporadic | 10 | 104088826 |
| answerals | CASE_NEUVU735HU6 | als | sporadic | 11 | 84591201 |
| answerals | CASE_NEUVV225XKB | als | sporadic | 13 | 88170541 |
| answerals | CASE_NEUVW680LPK | als | c9orf72 | 14 | 87448426 |
| answerals | CASE_NEUVW999FP9 | als | sporadic | 11 | 88473708 |
| answerals | CASE_NEUVX902YNL | als | c9orf72 | 5 | 81243471 |
| answerals | CTRL_NEUVZ050YX7 | ctrl | ctrl | 7 | 77251633 |
| answerals | CASE_NEUWD538KT3 | als | c9orf72 | 18 | 74315992 |
| answerals | CASE_NEUWD946RDA | als | sporadic | 8 | 102258678 |
| answerals | CASE_NEUWH380YHV | als | sporadic | 6 | 90420294 |
| answerals | CASE_NEUWH955FJF | als | sporadic | 6 | 91413950 |
| answerals | CASE_NEUWJ389FC7 | als | sporadic | 8 | 88864871 |
| answerals | CASE_NEUWM344ZLM | als | sod1 | 9 | 80462242 |
| answerals | CTRL_NEUWN092BVG | ctrl | ctrl | 7 | 74745103 |
| answerals | CASE_NEUWP426NBR | als | sporadic | 12 | 85098806 |
| answerals | CTRL_NEUWT164JRQ | ctrl | ctrl | 9 | 103798428 |
| answerals | CASE_NEUWX167DAH | als | sporadic | 5 | 87911909 |
| answerals | CASE_NEUWY079WUH | als | sporadic | 10 | 75802121 |
| answerals | CASE_NEUWZ614ARQ | als | sporadic | 10 | 72558498 |
| answerals | CTRL_NEUXC258VTR | ctrl | ctrl | 15 | 103588765 |
| answerals | CASE_NEUXD985ZU1 | als | sporadic | 8 | 92604037 |
| answerals | CASE_NEUXE491RMM | als | sporadic | 9 | 82047541 |
| answerals | CASE_NEUXG265ME9 | als | sporadic | 10 | 93938146 |
| answerals | CASE_NEUXH833LL4 | als | sporadic | 16 | 98829108 |
| answerals | CASE_NEUXP289KRC | als | sod1 | 11 | 106091617 |
| answerals | CASE_NEUXP495XE2 | als | sporadic | 13 | 100629256 |
| answerals | CASE_NEUXP595FFP | als | sporadic | 10 | 67304414 |
| answerals | CTRL_NEUXP955XW7 | ctrl | ctrl | 8 | 82124112 |
| answerals | CASE_NEUXV122FN3 | als | sporadic | 11 | 93817112 |
| answerals | CTRL_NEUXW311EFC | ctrl | ctrl | 8 | 56004456 |
| answerals | CASE_NEUXX361RUG | als | sporadic | 17 | 87796977 |
| answerals | CASE_NEUYC055XPZ | als | sporadic | 8 | 100062178 |
| answerals | CASE_NEUYC303AJY | als | sporadic | 3 | 86066890 |
| answerals | CASE_NEUYD306HAB | als | sporadic | 12 | 70161401 |
| answerals | CASE_NEUYG208KVV | als | sporadic | 8 | 80960435 |
| answerals | CASE_NEUYG298CA9 | als | sporadic | 9 | 87861391 |
| answerals | CASE_NEUYH924UCE | als | sporadic | 12 | 89527986 |
| answerals | CASE_NEUYJ705VN9 | als | sporadic | 12 | 83023955 |
| answerals | CASE_NEUYK029WUU | als | sporadic | 11 | 72565571 |
| answerals | CASE_NEUYL008GM4 | als | sporadic | 6 | 96506969 |
| answerals | CASE_NEUYL149PRF | als | sporadic | 24 | 85694260 |
| answerals | CTRL_NEUYM205MRL | ctrl | ctrl | 17 | 89833971 |
| answerals | CASE_NEUYP226CPW | als | sporadic | 5 | 95899428 |
| answerals | CASE_NEUYP235ZLD | als | tardbp | 22 | 85518723 |
| answerals | CASE_NEUYT193FFG | als | sporadic | 6 | 95425283 |
| answerals | CASE_NEUYY225MNZ | als | c9orf72 | 6 | 72067964 |
| answerals | CASE_NEUYY614DN8 | als | sporadic | 9 | 94478114 |
| answerals | CASE_NEUYY878JGP | als | sporadic | 21 | 97959785 |
| answerals | CASE_NEUZD231YZ6 | als | sporadic | 10 | 62725001 |
| answerals | CASE_NEUZE432DZM | als | sporadic | 3 | 89658284 |
| answerals | CASE_NEUZF321EW4 | als | sod1 | 13 | 88877063 |
| answerals | CASE_NEUZF473UEP | als | sporadic | 9 | 80160194 |
| answerals | CASE_NEUZJ053JGZ | als | sporadic | 11 | 90808999 |
| answerals | CASE_NEUZK054DP5 | als | sporadic | 10 | 84338071 |
| answerals | CASE_NEUZN836GME | als | sporadic | 18 | 107877753 |
| answerals | CASE_NEUZN936HJ9 | als | sporadic | 8 | 61443203 |
| answerals | CASE_NEUZP278MR4 | als | sporadic | 13 | 94669647 |
| answerals | CASE_NEUZT557DHF | als | sporadic | 11 | 86771528 |
| answerals | CASE_NEUZT902WVB | als | sporadic | 8 | 108245336 |
| answerals | CASE_NEUZV656DD1 | als | sporadic | 7 | 106453390 |
| answerals | CASE_NEUZW701NNF | als | c9orf72 | 10 | 65392843 |
| answerals | CASE_NEUZX521TKK | als | sporadic | 15 | 76703248 |
| answerals | CASE_NEUZX847VWV | als | sporadic | 5 | 89949563 |
| answerals | CASE_NEUZY128BJ2 | als | sporadic | 6 | 103216328 |
| answerals | CASE_NEUZY975XKL | als | sporadic | 12 | 75377931 |
| neurolincs.diMN | 00072034C01 | ctrl | ctrl | 4 | 88913175 |
| neurolincs.diMN | 00072034A01 | ctrl | ctrl | 7 | 87856433 |
| neurolincs.diMN | 00072028B01 | ctrl | ctrl | 5 | 84686602 |
| neurolincs.diMN | 00072028A01 | ctrl | ctrl | 6 | 86183708 |
| neurolincs.diMN | 00072010B02 | ctrl | ctrl | 10 | 71171884 |
| neurolincs.diMN | 00072010A02 | ctrl | ctrl | 7 | 72849067 |
| neurolincs.diMN | 00072002B02 | ctrl | ctrl | 8 | 81893396 |
| neurolincs.diMN | 00072002A02 | ctrl | ctrl | 8 | 78862140 |
| neurolincs.diMN | 00072007B01 | als | sporadic | 14 | 95655968 |
| neurolincs.diMN | 00072007A01 | als | sporadic | 16 | 86353118 |
| neurolincs.diMN | 00072006B01 | als | sporadic | 8 | 88663514 |
| neurolincs.diMN | 00072006A01 | als | sporadic | 8 | 87562150 |
| neurolincs.diMN | 00072019B02 | als | sporadic | 5 | 102600997 |
| neurolincs.diMN | 00072019A02 | als | sporadic | 4 | 81561535 |
| neurolincs.diMN | 00072001B02 | als | sporadic | 11 | 68658150 |
| neurolincs.diMN | 00072001A02 | als | sporadic | 5 | 92152108 |
| neurolincs.diMN | 00072029B01 | als | sod1 | 9 | 88644882 |
| neurolincs.diMN | 00072029A01 | als | sod1 | 9 | 69660338 |
| neurolincs.diMN | 00072018B02 | als | sod1 | 6 | 92304897 |
| neurolincs.diMN | 00072018A02 | als | sod1 | 5 | 78852703 |
| neurolincs.diMN | 00072008B02 | als | sod1 | 4 | 93585462 |
| neurolincs.diMN | 00072008A02 | als | sod1 | 6 | 80849799 |
| neurolincs.diMN | 00072015B01 | als | c9orf72 | 5 | 81357232 |
| neurolincs.diMN | 00072015A01 | als | c9orf72 | 8 | 80643118 |
| neurolincs.diMN | 00072012B01 | als | c9orf72 | 9 | 77973353 |
| neurolincs.diMN | 00072012A01 | als | c9orf72 | 9 | 96935001 |
| neurolincs.diMN | 00072014B02 | als | c9orf72 | 7 | 92196364 |
| neurolincs.diMN | 00072014A02 | als | c9orf72 | 3 | 83893881 |
| neurolincs.diMN | 00072013B02 | als | c9orf72 | 8 | 35176115 |
| neurolincs.diMN | 00072013A02 | als | c9orf72 | 6 | 77127001 |
| neurolincs.iMN | A-042-52iALS-004 | als | c9orf72 | 4 | 70623351 |
| neurolincs.iMN | A-042-52iALS-003 | als | c9orf72 | 3 | 54474248 |
| neurolincs.iMN | A-042-30iALS-004 | als | c9orf72 | 3 | 82501857 |
| neurolincs.iMN | A-042-30iALS-003 | als | c9orf72 | 3 | 62344831 |
| neurolincs.iMN | A-042-29iALS-004 | als | c9orf72 | 3 | 71722128 |
| neurolincs.iMN | A-042-29iALS-003 | als | c9orf72 | 4 | 67369943 |
| neurolincs.iMN | A-042-28iALS-005 | als | c9orf72 | 9 | 67180410 |
| neurolincs.iMN | A-042-28iALS-003 | als | c9orf72 | 8 | 50323795 |
| neurolincs.iMN | A-042-83iCTR-004 | ctrl | ctrl | 6 | 59263773 |
| neurolincs.iMN | A-042-83iCTR-003 | ctrl | ctrl | 4 | 59709899 |
| neurolincs.iMN | A-042-25iCTR-004 | ctrl | ctrl | 8 | 79504132 |
| neurolincs.iMN | A-042-25iCTR-003 | ctrl | ctrl | 7 | 61589963 |
| neurolincs.iMN | A-042-00iCTR-004 | ctrl | ctrl | 4 | 64065133 |
| neurolincs.iMN | A-042-00iCTR-003 | ctrl | ctrl | 3 | 58621934 |
| catanese | c9orf72_6 | als | c9orf72 | 12 | 44556823 |
| catanese | c9orf72_5 | als | c9orf72 | 18 | 44718862 |
| catanese | c9orf72_4 | als | c9orf72 | 16 | 48198617 |
| catanese | c9orf72_3 | als | c9orf72 | 11 | 49885755 |
| catanese | c9orf72_2 | als | c9orf72 | 9 | 50374657 |
| catanese | c9orf72_1 | als | c9orf72 | 12 | 52025076 |
| catanese | ctrl_3 | ctrl | ctrl | 4 | 41908415 |
| catanese | ctrl_2 | ctrl | ctrl | 8 | 41297925 |
| catanese | ctrl_1 | ctrl | ctrl | 10 | 43538558 |
| catanese | fus_6 | als | fus | 3 | 43123381 |
| catanese | fus_5 | als | fus | 5 | 43486913 |
| catanese | fus_4 | als | fus | 7 | 40817402 |
| catanese | fus_3 | als | fus | 10 | 47197324 |
| catanese | fus_2 | als | fus | 7 | 43048688 |
| catanese | fus_1 | als | fus | 11 | 45844283 |
| catanese | iso_3 | ctrl | iso | 9 | 48361792 |
| catanese | iso_2 | ctrl | iso | 9 | 47178499 |
| catanese | iso_1 | ctrl | iso | 6 | 44076352 |
| dafinca.c9orf72 | c9orf72_4 | als | c9orf72 | 3 | 42732664 |
| dafinca.c9orf72 | c9orf72_3 | als | c9orf72 | 3 | 41062026 |
| dafinca.c9orf72 | c9orf72_2 | als | c9orf72 | 2 | 48882465 |
| dafinca.c9orf72 | c9orf72_1 | als | c9orf72 | 3 | 46262015 |
| dafinca.c9orf72 | ctrl_1 | ctrl | ctrl | 5 | 45099717 |
| dafinca.c9orf72 | iso_7 | ctrl | iso | 1 | 36358941 |
| dafinca.c9orf72 | iso_6 | ctrl | iso | 2 | 36968802 |
| dafinca.c9orf72 | iso_5 | ctrl | iso | 1 | 39174051 |
| dafinca.c9orf72 | iso_4 | ctrl | iso | 4 | 35084625 |
| dafinca.c9orf72 | iso_3 | ctrl | iso | 4 | 45037650 |
| dafinca.c9orf72 | iso_2 | ctrl | iso | 4 | 41434677 |
| dafinca.c9orf72 | iso_1 | ctrl | iso | 2 | 43145131 |
| dafinca.tardbp | ctrl_4 | ctrl | ctrl | 5 | 13922252 |
| dafinca.tardbp | ctrl_3 | ctrl | ctrl | 11 | 18207019 |
| dafinca.tardbp | ctrl_2 | ctrl | ctrl | 5 | 17409430 |
| dafinca.tardbp | ctrl_1 | ctrl | ctrl | 7 | 15358338 |
| dafinca.tardbp | tardbp_6 | als | tardbp | 3 | 18450547 |
| dafinca.tardbp | tardbp_5 | als | tardbp | 6 | 16996133 |
| dafinca.tardbp | tardbp_4 | als | tardbp | 5 | 17702995 |
| dafinca.tardbp | tardbp_3 | als | tardbp | 5 | 18246091 |
| dafinca.tardbp | tardbp_2 | als | tardbp | 8 | 16856043 |
| dafinca.tardbp | tardbp_1 | als | tardbp | 5 | 17886729 |
| wang | iso_2 | ctrl | iso | 9 | 25470901 |
| wang | iso_1 | ctrl | iso | 16 | 25318736 |
| wang | sod1_2 | als | sod1 | 18 | 25959947 |
| wang | sod1_1 | als | sod1 | 14 | 26086164 |
| kiskinis | iso_3 | ctrl | iso | 12 | 14683349 |
| kiskinis | iso_2 | ctrl | iso | 9 | 9190834 |
| kiskinis | iso_1 | ctrl | iso | 7 | 10724700 |
| kiskinis | sod1_2 | als | sod1 | 38 | 13383139 |
| kiskinis | sod1_1 | als | sod1 | 28 | 7037516 |
| sommer | c9orf72_1 | als | c9orf72 | 3 | 40465430 |
| sommer | c9orf72_2 | als | c9orf72 | 4 | 38631160 |
| sommer | c9orf72_3 | als | c9orf72 | 4 | 41347502 |
| sommer | c9orf72_4 | als | c9orf72 | 2 | 50500461 |
| sommer | c9orf72_5 | als | c9orf72 | 3 | 40439998 |
| sommer | c9orf72_6 | als | c9orf72 | 3 | 46224895 |
| sommer | ctrl_1 | ctrl | ctrl | 2 | 41738904 |
| sommer | ctrl_2 | ctrl | ctrl | 5 | 46986721 |
| sommer | ctrl_3 | ctrl | ctrl | 7 | 43178218 |
| sommer | ctrl_4 | ctrl | ctrl | 3 | 39573053 |
| sommer | ctrl_5 | ctrl | ctrl | 4 | 40502175 |
| sommer | ctrl_6 | ctrl | ctrl | 4 | 36822732 |
| desantis | ctrl_3 | ctrl | ctrl | 5 | 29102751 |
| desantis | ctrl_2 | ctrl | ctrl | 2 | 18402574 |
| desantis | ctrl_1 | ctrl | ctrl | 8 | 27289409 |
| desantis | fus_3 | als | fus | 9 | 26858355 |
| desantis | fus_2 | als | fus | 2 | 16997472 |
| desantis | fus_1 | als | fus | 8 | 24909519 |
| smith | tardbp_3 | als | tardbp | 1 | 7448645 |
| smith | tardbp_2 | als | tardbp | 1 | 7455838 |
| smith | ctrl_2 | ctrl | ctrl | 1 | 7445173 |
| smith | tardbp_1 | als | tardbp | 0 | 7471156 |
| smith | ctrl_1 | ctrl | ctrl | 0 | 7248337 |
ipsc_mn_als_datasets.starfusion.als.count = ipsc_mn_als_datasets.starfusion %>% filter(condition == "als") %>% count(breakpoints, name = "als_yes")
ipsc_mn_als_datasets.starfusion.ctrl.count = ipsc_mn_als_datasets.starfusion %>% filter(condition == "ctrl") %>% count(breakpoints, name = "ctrl_yes")
ipsc_mn_als_datasets.starfusion.als_ctrl.prop = ipsc_mn_als_datasets.starfusion.als.count %>% full_join(ipsc_mn_als_datasets.starfusion.ctrl.count) %>% replace(is.na(.),0) %>%
mutate(als_total = 360, ctrl_total = 90)
ipsc_mn_als_datasets.starfusion.als_ctrl.burden = ipsc_mn_als_datasets.starfusion.als_ctrl.prop %>% rowwise() %>%
mutate(p_value = ClusterBurden::burden_test(n1 = als_yes, n2 = ctrl_yes, ss1 = als_total, ss2 = ctrl_total),
odds_ratio = ClusterBurden::burden_test(n1 = als_yes, n2 = ctrl_yes, ss1 = als_total, ss2 = ctrl_total, pval = FALSE)$estimate[1],
lower_ci = ClusterBurden::burden_test(n1 = als_yes, n2 = ctrl_yes, ss1 = als_total, ss2 = ctrl_total, pval = FALSE)$conf.int[1],
upper_ci = ClusterBurden::burden_test(n1 = als_yes, n2 = ctrl_yes, ss1 = als_total, ss2 = ctrl_total, pval = FALSE)$conf.int[2])
als_ctrl.voila = read_voila_het(here(proj_path,"splicing/majiq_polyA/voila-tsv/als_vs_ctrl.tsv"), grp1 = "als", grp2 = "ctrl")
als_ctrl.voila.splicing_genes = als_ctrl.voila %>% filter(changing_dpsi0.1 == TRUE) %>% distinct(gene_name) %>% pull(gene_name)
ipsc_mn_als_datasets.starfusion.als_ctrl.burden_table = ipsc_mn_als_datasets.starfusion.als_ctrl.burden %>% left_join(distinct(select(ipsc_mn_als_datasets.starfusion, breakpoints, fusion_name, fusion_type))) %>% arrange(p_value) %>%
mutate(gene1 = str_split_fixed(fusion_name, "--",2)[,1], gene2 = str_split_fixed(fusion_name, "--",2)[,2], alterated_splicing = case_when(gene1 %in% als_ctrl.voila.splicing_genes | gene2 %in% als_ctrl.voila.splicing_genes ~ "yes", TRUE ~ "")) %>%
select(fusion_name, breakpoints, fusion_type, als_number = als_yes, ctrl_number = ctrl_yes, odds_ratio, lower_ci, upper_ci, p_value, alterated_splicing)
kbl(ipsc_mn_als_datasets.starfusion.als_ctrl.burden_table) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), fixed_thead = T) %>% scroll_box(width = "100%", height = "500px")| fusion_name | breakpoints | fusion_type | als_number | ctrl_number | odds_ratio | lower_ci | upper_ci | p_value | alterated_splicing |
|---|---|---|---|---|---|---|---|---|---|
| LINC01572–PMFBP1 | 16:72284572:-_16:72164916:- | Neighbours | 78 | 7 | 3.2728937 | 1.6047187 | Inf | 0.0011203 | |
| Z68871.1–LINC00630 | X:102905737:+_X:102839801:+ | Overlapping Neighbours | 181 | 29 | 2.1234663 | 1.3759543 | Inf | 0.0014416 | |
| AC010332.1–ZNF880 | 19:52392788:+_19:52373111:+ | Local Rearrangement | 200 | 35 | 1.9613446 | 1.2874724 | Inf | 0.0032937 | |
| KRTAP5-AS1–AP000867.5 | 11:1598289:+_11:71563684:- | Distant Proximity | 121 | 18 | 2.0221779 | 1.2305056 | Inf | 0.0075401 | |
| C15orf40–HOMER2 | 15:83010237:-_15:82892841:- | Neighbours | 17 | 0 | Inf | 1.3333228 | Inf | 0.0208346 | |
| CAVIN4–TMEFF1 | 9:100585927:+_9:100498765:+ | Local Rearrangement | 165 | 30 | 1.6903608 | 1.0980652 | Inf | 0.0208959 | |
| CAVIN4–MSANTD3-TMEFF1 | 9:100585927:+_9:100498765:+ | Local Rearrangement | 165 | 30 | 1.6903608 | 1.0980652 | Inf | 0.0208959 | |
| LARS2–LIMD1 | 3:45524108:+_3:45636150:+ | Neighbours | 94 | 15 | 1.7648808 | 1.0352138 | Inf | 0.0385663 | |
| SPRY4-AS1–LINC01844 | 5:142581914:+_5:142745208:+ | Neighbours | 21 | 1 | 5.5008163 | 1.0360787 | Inf | 0.0441840 | |
| NREP–HMGN1P13 | 5:111735430:-_5:111572325:- | Neighbours | 53 | 8 | 1.7675789 | 0.8839976 | Inf | 0.0979401 | |
| CRYBB2P1–GRK3 | 22:25520733:+_22:25604377:+ | Neighbours | 10 | 0 | Inf | 0.7222905 | Inf | 0.1046809 | |
| CRYBB2P1–GRK3 | 22:25459515:+_22:25604377:+ | Neighbours | 32 | 4 | 2.0948470 | 0.8181814 | Inf | 0.1166954 | |
| PTCHD4–AL353138.1 | 6:48008634:-_6:48069926:- | Local Rearrangement | 41 | 6 | 1.7974036 | 0.8173929 | Inf | 0.1297229 | |
| CRIPT–SOCS5 | 2:46619681:+_2:46758519:+ | Neighbours | 9 | 0 | Inf | 0.6372242 | Inf | 0.1315222 | |
| SUB1–NPR3 | 5:32591685:+_5:32724698:+ | Neighbours | 14 | 1 | 3.5943007 | 0.6480436 | Inf | 0.1624562 | |
| NKAPP1–RHOXF1 | X:120244764:-_X:120112914:- | Neighbours | 8 | 0 | Inf | 0.5528235 | Inf | 0.1651500 | |
| ZNF350-AS1–ZNF613 | 19:51949235:+_19:51948593:+ | Local Rearrangement | 108 | 22 | 1.3238770 | 0.8260146 | Inf | 0.1819186 | |
| PHOSPHO2–SSB | 2:169697531:+_2:169800952:+ | Neighbours | 28 | 4 | 1.8111304 | 0.6999659 | Inf | 0.1945447 | |
| KLHL23–SSB | 2:169697531:+_2:169800952:+ | Neighbours | 28 | 4 | 1.8111304 | 0.6999659 | Inf | 0.1945447 | |
| AC119396.2–INSR | 19:7390576:-_19:7267896:- | Neighbours | 31 | 5 | 1.6002867 | 0.6737518 | Inf | 0.2356393 | |
| LINC01572–PMFBP1 | 16:72284577:-_16:72164916:- | Neighbours | 16 | 2 | 2.0438043 | 0.5539893 | Inf | 0.2658738 | |
| AL035409.2–ST6GALNAC5 | 1:77068843:+_1:77044204:+ | Local Rearrangement | 34 | 6 | 1.4589710 | 0.6548855 | Inf | 0.2747451 | |
| USP22–RN7SL5P | 17:21000941:-_9:9442093:+ | Inter Chromosomal | 29 | 5 | 1.4882051 | 0.6230567 | Inf | 0.2903729 | |
| CCDC122–ENOX1 | 13:43874842:-_13:43667544:- | Neighbours | 84 | 18 | 1.2169099 | 0.7323742 | Inf | 0.3003889 | |
| CXXC5–PSD2 | 5:139648845:+_5:139809391:+ | Distant Proximity | 15 | 2 | 1.9107102 | 0.5134713 | Inf | 0.3047402 | |
| DR1–FNBP1L | 1:93354071:+_1:93499468:+ | Neighbours | 10 | 1 | 2.5389621 | 0.4341852 | Inf | 0.3188009 | |
| AC068446.2–NBEAP1 | 15:21298706:-_15:20671268:- | Distant Proximity | 5 | 0 | Inf | 0.3042365 | Inf | 0.3258509 | |
| AC068446.2–AC060814.4 | 15:21324988:-_15:21328980:- | Local Rearrangement | 5 | 0 | Inf | 0.3042365 | Inf | 0.3258509 | |
| CAVIN4–MSANTD3-TMEFF1 | 9:100578551:+_9:100498765:+ | Local Rearrangement | 5 | 0 | Inf | 0.3042365 | Inf | 0.3258509 | |
| CAVIN4–TMEFF1 | 9:100578551:+_9:100498765:+ | Local Rearrangement | 5 | 0 | Inf | 0.3042365 | Inf | 0.3258509 | |
| SEPTIN7P2–PSPH | 7:45768660:-_7:56021231:- | Distant Proximity | 19 | 3 | 1.6142971 | 0.5366688 | Inf | 0.3262606 | |
| PSPC1–ZMYM5 | 13:19730239:-_13:19835689:- | Local Rearrangement | 52 | 11 | 1.2120054 | 0.6523621 | Inf | 0.3625712 | |
| YAF2–RYBP | 12:42238155:-_3:72446621:- | Inter Chromosomal | 9 | 1 | 2.2788627 | 0.3817097 | Inf | 0.3730935 | |
| C1QTNF3-AMACR–AC138409.2 | 5:34124418:-_5:34182867:- | Local Rearrangement | 9 | 1 | 2.2788627 | 0.3817097 | Inf | 0.3730935 | |
| LINC01145–SRGAP2B | 1:145215639:-_1:145093443:- | Neighbours | 13 | 2 | 1.6468051 | 0.4332582 | Inf | 0.3946244 | |
| CRYBB2P1–GRK3 | 22:25520733:+_22:25644592:+ | Neighbours | 17 | 3 | 1.4362559 | 0.4709196 | Inf | 0.4074672 | |
| FNBP1L–MTF2 | 1:93448305:+_1:93110230:+ | Distant Proximity | 4 | 0 | Inf | 0.2236690 | Inf | 0.4082290 | |
| MFNG–ELFN2 | 22:37476896:-_22:37375996:- | Neighbours | 4 | 0 | Inf | 0.2236690 | Inf | 0.4082290 | |
| RARB–AC092422.1 | 3:25174575:+_3:25060125:+ | Local Rearrangement | 4 | 0 | Inf | 0.2236690 | Inf | 0.4082290 | |
| PCMTD1–PXDNL | 8:51898930:-_8:51654760:- | Neighbours | 4 | 0 | Inf | 0.2236690 | Inf | 0.4082290 | |
| LINC01933–AC008571.2 | 5:152267355:+_5:152537704:+ | Distant Proximity | 8 | 1 | 2.0201305 | 0.3296629 | Inf | 0.4341726 | |
| NREP–HMGN1P13 | 5:111677940:-_5:111572325:- | Neighbours | 28 | 6 | 1.1803022 | 0.5211467 | Inf | 0.4620774 | |
| AC012414.4–AC012414.2 | 15:20755930:-_15:20761158:- | Local Rearrangement | 11 | 2 | 1.3858939 | 0.3542338 | Inf | 0.4999902 | |
| MFSD14B–AL691447.2 | 9:94438528:+_9:94338836:+ | Local Rearrangement | 7 | 1 | 1.7629706 | 0.2781994 | Inf | 0.5019998 | |
| AC092745.5–AC092745.2 | 12:8251507:+_12:8368982:+ | Overlapping Neighbours | 3 | 0 | Inf | 0.1453421 | Inf | 0.5111438 | |
| PSPC1–ZMYM5 | 13:19741565:-_13:19835689:- | Local Rearrangement | 3 | 0 | Inf | 0.1453421 | Inf | 0.5111438 | |
| LINC00674–AMZ2 | 17:68114525:+_17:68250188:+ | Neighbours | 3 | 0 | Inf | 0.1453421 | Inf | 0.5111438 | |
| AC022140.1–AC099499.1 | 5:25445820:-_5:25298609:- | Distant Proximity | 3 | 0 | Inf | 0.1453421 | Inf | 0.5111438 | |
| MRPL14–AL109615.3 | 6:44114077:-_6:44001116:- | Neighbours | 3 | 0 | Inf | 0.1453421 | Inf | 0.5111438 | |
| KIAA1958–SNX30 | 9:112575251:+_9:112804776:+ | Neighbours | 3 | 0 | Inf | 0.1453421 | Inf | 0.5111438 | |
| TMEM164–RTL9 | X:110171520:+_X:110445153:+ | Distant Proximity | 3 | 0 | Inf | 0.1453421 | Inf | 0.5111438 | |
| AL353138.1–PTCHD4 | 6:48111049:-_6:48009114:- | Neighbours | 293 | 73 | 1.0183603 | 0.5851179 | Inf | 0.5285463 | |
| LINC01315–TCF20 | 22:42368715:-_22:42215341:- | Neighbours | 34 | 8 | 1.0688608 | 0.5190433 | Inf | 0.5294393 | |
| PRDM2–KAZN | 1:13843107:+_1:14180435:+ | Neighbours | 18 | 4 | 1.1312776 | 0.4170870 | Inf | 0.5418132 | |
| BBOX1-AS1–SLC5A12 | 11:27151050:-_11:26712706:- | Distant Proximity | 14 | 3 | 1.1730102 | 0.3739383 | Inf | 0.5479357 | |
| AC022523.1–LINC00923 | 15:98046667:-_15:97758661:- | Distant Proximity | 14 | 3 | 1.1730102 | 0.3739383 | Inf | 0.5479357 | |
| AC007318.1–RAB1A | 2:65227485:-_2:65104806:- | Neighbours | 6 | 1 | 1.5072445 | 0.2273381 | Inf | 0.5761020 | |
| SHROOM2–WWC3 | X:9944913:+_X:10063445:+ | Neighbours | 17 | 4 | 1.0654241 | 0.3897934 | Inf | 0.5860321 | |
| USP22–RN7SL2 | 17:21000941:-_14:49862816:- | Inter Chromosomal | 36 | 9 | 1.0000000 | 0.5019715 | Inf | 0.5896286 | |
| USP22–AL627171.2 | 17:21000941:-_14:49862816:- | Inter Chromosomal | 36 | 9 | 1.0000000 | 0.5019715 | Inf | 0.5896286 | |
| AC096642.2–LYPLAL1 | 1:219295151:+_1:219193082:+ | Local Rearrangement | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| MIR3659HG–AL390839.2 | 1:38047614:+_1:38209271:+ | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| SLIRP–ADCK1 | 14:77715879:+_14:77818968:+ | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| ADAMTSL3–SH3GL3 | 15:83704508:+_15:83559253:+ | Local Rearrangement | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| AC110023.1–AC091078.1 | 15:93592733:+_15:93553605:+ | Local Rearrangement | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| LINC01572–PMFBP1 | 16:72284577:-_16:72171268:- | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| LINC01572–PMFBP1 | 16:72284577:-_16:72174070:- | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| CDH13–HSBP1 | 16:83486655:+_16:83808680:+ | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| USP22–RN7SL4P | 17:21000941:-_3:15738548:+ | Inter Chromosomal | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| ARL17B–KANSL1 | 17:46352820:-_17:46094701:- | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| SNHG16–METTL23 | 17:76614005:+_17:76732978:+ | Distant Proximity | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| SNHG16–AC005837.2 | 17:76614005:+_17:76732978:+ | Distant Proximity | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| RNF138–MEP1B | 18:32092886:+_18:32204182:+ | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| MYDGF–SEMA6B | 19:4659931:-_19:4558489:- | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| AC007318.1–RAB1A | 2:65227428:-_2:65104806:- | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| RNF144A–AC013460.1 | 2:7075684:+_2:7421184:+ | Distant Proximity | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| MBOAT2–KIDINS220 | 2:9003540:-_2:8827129:- | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| CHMP4B–DEFB115 | 20:33811658:+_20:31249509:+ | Distant Proximity | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| C20orf194–PIAS1 | 20:3407475:-_15:68086306:+ | Inter Chromosomal | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| PPM1F–MAPK1 | 22:21931148:-_22:21807846:- | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| CRYBB2P1–GRK3 | 22:25520733:+_22:25667739:+ | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| SYN3–RTCB | 22:32596674:-_22:32408833:- | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| AC068756.1–AC108690.1 | 3:80761438:-_3:80633971:- | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| AC026410.3–RAPGEF1 | 5:80351234:-_9:131650949:- | Inter Chromosomal | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | yes |
| MAILR–ATP6V1C1 | 8:102880058:+_8:103040798:+ | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| LINC00032–EQTN | 9:27277551:-_9:27286362:- | Overlapping Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| ERMP1–KIAA2026 | 9:5787061:-_9:5914062:- | Local Rearrangement | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| BHLHB9–LINC00630 | X:102721027:+_X:102826969:+ | Neighbours | 2 | 0 | Inf | 0.0718293 | Inf | 0.6396437 | |
| PFKFB3–LINC02649 | 10:6226365:+_10:6326546:+ | Neighbours | 23 | 6 | 0.9555832 | 0.4134739 | Inf | 0.6453096 | |
| BTF3L4–ZFYVE9 | 1:52064938:+_1:52216369:+ | Neighbours | 5 | 1 | 1.2529300 | 0.1772958 | Inf | 0.6553631 | |
| EFL1P1–AC243562.2 | 15:84126600:+_15:84389732:+ | Distant Proximity | 5 | 1 | 1.2529300 | 0.1772958 | Inf | 0.6553631 | |
| LINC01572–PMFBP1 | 16:72284572:-_16:72171268:- | Neighbours | 5 | 1 | 1.2529300 | 0.1772958 | Inf | 0.6553631 | |
| TIAM2–SCAF8 | 6:154944206:+_6:154773989:+ | Overlapping Neighbours | 5 | 1 | 1.2529300 | 0.1772958 | Inf | 0.6553631 | |
| AC009315.1–FSIP2 | 2:185434191:+_2:185739346:+ | Distant Proximity | 19 | 5 | 0.9473240 | 0.3790265 | Inf | 0.6580759 | |
| AC010332.1–ZNF880 | 19:52392776:+_19:52315951:+ | Local Rearrangement | 8 | 2 | 1.0000000 | 0.2381207 | Inf | 0.6784890 | |
| BHLHB9–LINC00630 | X:102721091:+_X:102826969:+ | Neighbours | 8 | 2 | 1.0000000 | 0.2381207 | Inf | 0.6784890 | |
| LINC01145–SRGAP2 | 1:145215639:-_1:206205429:+ | Distant Proximity | 11 | 3 | 0.9142135 | 0.2790496 | Inf | 0.6997665 | |
| AC068446.2–AC060814.4 | 15:21324988:-_15:21330231:- | Local Rearrangement | 4 | 1 | 1.0000000 | 0.1284236 | Inf | 0.7377411 | |
| LINC01572–PMFBP1 | 16:72249163:-_16:72164916:- | Neighbours | 4 | 1 | 1.0000000 | 0.1284236 | Inf | 0.7377411 | |
| RPL37A–AC073321.1 | 2:216500031:+_2:216610744:+ | Neighbours | 4 | 1 | 1.0000000 | 0.1284236 | Inf | 0.7377411 | |
| MED27–RAPGEF1 | 9:131884058:-_9:131650949:- | Distant Proximity | 4 | 1 | 1.0000000 | 0.1284236 | Inf | 0.7377411 | yes |
| AL355987.4–GPI | 9:136802786:+_19:34393248:+ | Inter Chromosomal | 34 | 10 | 0.8346905 | 0.4270443 | Inf | 0.7554429 | |
| CCDC183–GPI | 9:136802786:+_19:34393248:+ | Inter Chromosomal | 34 | 10 | 0.8346905 | 0.4270443 | Inf | 0.7554429 | |
| AL355987.2–GPI | 9:136802786:+_19:34393248:+ | Inter Chromosomal | 34 | 10 | 0.8346905 | 0.4270443 | Inf | 0.7554429 | |
| AEBP2–AC024901.1 | 12:19720691:+_12:19923198:+ | Neighbours | 9 | 3 | 0.7441212 | 0.2171197 | Inf | 0.7969835 | |
| PTS–LINC02762 | 11:112237506:+_11:112360069:+ | Neighbours | 6 | 2 | 0.7462908 | 0.1628979 | Inf | 0.7984087 | |
| AC009315.1–FSIP2 | 2:185502739:+_2:185739346:+ | Distant Proximity | 6 | 2 | 0.7462908 | 0.1628979 | Inf | 0.7984087 | |
| SLC16A1-AS1–LRIG2 | 1:112960575:+_1:113091318:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| MIIP–MFN2 | 1:12022917:+_1:12014257:+ | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| LINC01138–FCGR1CP | 1:148459602:-_1:143880437:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| RABGAP1L–MED14 | 1:174278779:+_X:40729345:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CEP350–TDRD5 | 1:179987286:+_1:179690696:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CNIH3–WDR26 | 1:224434862:+_1:224431781:- | Overlapping Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AKT3–RPS10 | 1:243504348:-_6:34426060:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AKT3–RPS10 | 1:243504388:-_6:34426060:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| GMEB1–SMG1 | 1:28683740:+_16:18896956:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ZFP69B–LIFR | 1:40457071:+_5:38511964:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PLK3–RPS8 | 1:44802855:+_1:44778000:+ | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| BTF3L4–ZFYVE9 | 1:52064938:+_1:52199251:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AL669831.3–DCX | 1:631066:-_X:111299018:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| INPP5F–NOVA1 | 10:119823199:+_14:26448963:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| BX322639.1–CCNYL2 | 10:42360949:-_10:42433354:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| BX322639.1–CCNYL2 | 10:42367816:-_10:42433354:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AGAP4–PARGP1 | 10:45841653:-_10:45964871:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| MRPS16–CFAP70 | 10:73251763:-_10:73256416:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| GLUD1P3–LMBR1 | 10:73730873:+_7:156826744:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| POLR3A–HMGCS1 | 10:78002197:-_5:43297166:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| NUTM2B-AS1–SFTPA2 | 10:79766271:-_10:79559506:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| NRG3–KRTAP5-AS1 | 10:81876163:+_11:1597248:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| NUTM2A-AS1–GLUD1 | 10:87326630:-_10:87076656:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| NKAPD1–CPSF3 | 11:112075643:+_2:9441818:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ZBTB16–NXPE2 | 11:114187038:+_11:114679657:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| JAM3–PTPN11 | 11:134069159:+_12:112446276:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| DNAJC24–IMMP1L | 11:31370859:+_11:31433570:- | Overlapping Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PTDSS2–DLGAP4 | 11:448419:+_20:36525851:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PHF21A–SPCS2 | 11:46076754:-_11:74965034:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PTDSS2–DAZAP1 | 11:479152:+_19:1417500:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| MALAT1–ADGRV1 | 11:65505019:+_5:90720935:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PACS1–UQCC2 | 11:66210451:+_6:33700513:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| RBM14–C11orf80 | 11:66617057:+_11:66759043:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | yes |
| UBE3B–MYCN | 12:109526416:+_2:15945493:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CFAP73–TSPAN4 | 12:113152887:+_11:847201:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| NCOR2–AC048337.1 | 12:124362126:-_12:121391970:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | yes |
| NCOR2–RNF34 | 12:124362126:-_12:121416159:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | yes |
| AEBP2–AC024901.1 | 12:19518113:+_12:19923198:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| BICD1–FGD4 | 12:32107544:+_12:32564137:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TUBA1A–PTMS | 12:49185036:-_12:6770157:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TUBA1A–NEFM | 12:49185049:-_8:24917437:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CPSF6–JAG2 | 12:69262562:+_14:105141329:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CPSF6–ADGRB3 | 12:69262562:+_6:69372406:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CPSF6–KBTBD11 | 12:69262562:+_8:2006545:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TBC1D15–RAB21 | 12:71885021:+_12:71782031:+ | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PPP1R12A–CAPS2-AS1 | 12:79817394:-_12:75250493:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ATP2B1–PCSK2 | 12:89627678:-_20:17436708:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PSPC1–ZMYM5 | 13:19772242:-_13:19835689:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PSPC1–ZMYM5 | 13:19782386:-_13:19852190:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PSPC1–ZMYM5 | 13:19782386:-_13:19862466:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TPTE2P5–MRPS31 | 13:40908159:-_13:40767033:- | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| VWA8–SH3YL1 | 13:41865736:-_2:230044:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| FARP1–IPO5 | 13:98213413:+_13:98006130:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| SLC38A6–PRKCH | 14:61030523:+_14:61391225:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC012414.4–IGHV1OR15-6 | 15:20755930:-_15:20639759:- | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC012414.4–AC100757.2 | 15:20755930:-_15:22360628:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC124312.1–ATP2B1 | 15:24982437:+_12:89656107:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TTBK2–SMG1P3 | 15:42827928:-_16:21487616:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC012405.1–AC073941.1 | 15:46410353:+_15:46791282:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| MIR4713HG–GLDN | 15:51037681:+_15:51377449:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| MIR4713HG–GLDN | 15:51037681:+_15:51383785:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TLN2–TLN1 | 15:62833629:+_9:35698679:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| UBE2Q2P2–AC243562.1 | 15:82355374:+_15:84394809:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| C15orf40–HOMER2 | 15:83008548:-_15:82892841:- | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| IGF1R–LUNAR1 | 15:98708107:+_15:99024600:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| IGF1R–SYNM | 15:98708107:+_15:99113591:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PDXDC1–NOMO1 | 16:15030056:+_16:14838407:+ | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PKD1P6–MAZ | 16:15133264:-_16:29808230:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| UQCRC2–PJA2 | 16:21976243:+_5:109356026:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| DNASE1–PTBP1 | 16:3612006:+_19:799413:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| UTP4–SNTB2 | 16:69143389:+_16:69245602:+ | Overlapping Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ANKRD11–CAMK2B | 16:89418284:-_7:44263064:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | yes |
| DEF8–OSGEP | 16:89949513:+_14:20449301:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | yes |
| C16orf72–AC012178.1 | 16:9103259:+_16:9461042:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| SUZ12P1–AC005562.1 | 17:30709811:+_17:30631755:+ | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | yes |
| AC138207.8–NF1 | 17:31045549:+_17:31155983:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ARL17A–KANSL1 | 17:46570759:-_17:46094701:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| NPEPPS–TBC1D3I | 17:47592545:+_17:36262986:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| SPOP–MSI2 | 17:49677933:-_17:57401379:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| GDPD1–GIT2 | 17:59272836:+_12:109961685:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TANC2–PSMA3 | 17:63319090:+_14:58247750:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| VPS53–GLOD4 | 17:710533:-_17:785977:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ATP1B2–AL627171.2 | 17:7656775:+_14:49862816:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| FAAP100–TRIOBP | 17:81544004:-_22:37733298:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TBCD–ATP8B3 | 17:82911789:+_19:1800449:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| NTN1–AL121594.1 | 17:9221242:+_14:35266727:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| DOK6–AC006305.1 | 18:69599498:+_18:56181474:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC124254.2–AC123786.1 | 18:77422024:+_18:77613183:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| EIF3G–ENO4 | 19:10118668:-_10:116862799:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TCF3–CCDC57 | 19:1646355:-_17:82101866:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ZNF493–CRCP | 19:21397267:+_7:66127704:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC092279.1–RBM39 | 19:24049014:+_20:35725155:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| NFIC–CTBP1 | 19:3359685:+_4:1241519:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ZBTB7A–WDR59 | 19:4053971:-_16:74956610:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ZNF175–SRP68 | 19:51581882:+_17:76040474:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ZNF846–ZNF561-AS1 | 19:9785938:-_19:9627716:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | yes |
| KLHL23–SSB | 2:169695247:+_2:169800952:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC074286.1–AC092162.2 | 2:177094575:-_2:176812193:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC021851.1–NUP35 | 2:183182680:+_2:183151508:+ | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC009315.1–FSIP2 | 2:185434187:+_2:185737013:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC009315.1–FSIP2 | 2:185502739:+_2:185737013:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC097500.1–LINC01473 | 2:185950644:-_2:186086370:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| WDR75–KLF7 | 2:189441578:+_2:207124404:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PUM2–SMAD5 | 2:20327310:-_5:136160856:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| MAPRE3–ACYP2 | 2:26970802:+_2:54135453:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| LTBP1–BIRC6 | 2:33021206:+_2:32406499:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CRIPT–SOCS5 | 2:46648138:+_2:46758519:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| SPTBN1–RTN4 | 2:54558887:+_2:54987698:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC007318.1–RAB1A | 2:65227481:-_2:65104806:- | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| RNF144A–AC013460.1 | 2:6997061:+_2:7421184:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AL050403.2–PLXDC2 | 20:10673025:+_10:20211669:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PTPRA–ATF2 | 20:2965202:+_2:175151158:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| FASTKD5–CARS2 | 20:3159766:-_13:110701555:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TTI1–VSTM2L | 20:37996375:-_20:37931635:+ | Local Inversion | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| SULF2–CKS1B | 20:47736703:-_1:154978725:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| VAPB–APCDD1L-DT | 20:58418363:+_20:58547812:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CDH4–ERICH1 | 20:61254937:+_8:674047:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| VPS26C–TTC3 | 21:37267238:-_21:37108392:+ | Local Inversion | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| GUSBP11–AC113385.3 | 22:23659865:-_5:100381398:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CRYBB2P1–GRK3 | 22:25459515:+_22:25661576:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| GALR3–ANKRD54 | 22:37823765:+_22:37838593:- | Local Inversion | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| RAB43–GORASP2 | 3:129121286:-_2:170948350:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| LINC02021–COL6A4P2 | 3:130112744:+_3:130212823:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ANAPC13–AMOTL2 | 3:134482806:-_3:134371494:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC046134.2–CLSTN2 | 3:139583880:+_3:140175951:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TFDP2–XRN1 | 3:142101735:-_3:142365366:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| METTL6–SH3BP5 | 3:15415772:-_3:15304231:- | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| EGFEM1P–KANSL1L | 3:168824925:+_2:210154611:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| SLC7A14-AS1–AC061708.1 | 3:170708194:+_3:170994873:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ERC2–CDC42BPA | 3:56007181:-_1:227048010:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| UBA3–STRAP | 3:69077798:-_12:15890597:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ZNF717–RPL23AP49 | 3:75741276:-_3:75625153:- | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC068756.1–AC108690.1 | 3:80761458:-_3:80633971:- | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| LINC02050–LINC02027 | 3:80770955:+_3:81095112:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC107029.2–COL8A1 | 3:99635662:+_3:99744897:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC108865.1–AC110772.2 | 4:186891368:+_4:187019821:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PCDH7–LINC02497 | 4:30920369:+_4:31176621:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CFAP299–BMP3 | 4:80870135:+_4:81045738:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| EPB41L4A–NREP | 5:112168739:-_5:111735507:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AP3S1–LVRN | 5:115870128:+_5:115983287:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| LYRM7–CDC42SE2 | 5:131171038:+_5:131315976:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| UIMC1–UBE2B | 5:177022464:-_5:134390225:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| C1QTNF3-AMACR–AC138409.2 | 5:34020587:-_5:34182867:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TTC33–PRKAA1 | 5:40728345:-_5:40777586:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| RTN4IP1–LINC02532 | 6:106583328:-_6:106718242:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CEP57L1–AFG1L | 6:109095575:+_6:108519697:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CEP57L1–TTC6 | 6:109146937:+_14:37807320:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| NEDD9–AC018630.4 | 6:11232504:-_12:11047188:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| RNF217–TPD52L1 | 6:125045444:+_6:125220078:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AL133346.1–AL021408.1 | 6:131951254:+_6:132098931:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TBPL1–AHI1 | 6:133953425:+_6:135290525:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CCDC170–TBC1D32 | 6:151615679:+_6:121239188:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ATXN1–ZFYVE27 | 6:16753233:-_10:97744729:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AL662797.1–TUBA1A | 6:30723725:-_12:49185063:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| RNF5–TSBP1-AS1 | 6:32180126:+_6:32365780:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AL021368.4–UBE4B | 6:57959028:-_1:10161142:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| KHDRBS2-OT1–KHDRBS2 | 6:61652255:-_6:61707403:- | Overlapping Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| EEF1A1–RPS11 | 6:73519337:-_19:49497194:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AL391840.3–SH3BGRL2 | 6:79631633:+_6:79673614:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| EEF1E1-BLOC1S5–SMIM13 | 6:8097267:-_6:11134403:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CNPY4–RPS6KC1 | 7:100119862:+_1:213242569:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| FAM185A–LRRC17 | 7:102808351:+_7:102933774:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| FBXL13–AC105052.5 | 7:102822040:-_7:102703527:- | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| RINT1–AC073073.1 | 7:105548710:+_7:105530509:+ | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| MTPN–CHRM2 | 7:135977029:-_7:137014820:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| IQCE–SH3RF1 | 7:2573488:+_4:169156679:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| HOTAIRM1–WDR75 | 7:27096388:+_2:189458753:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| OGDH–ZNF816-ZNF321P | 7:44681848:+_19:52929414:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC079781.5–BBS2 | 7:97854580:-_16:56485738:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| BUD31–PDAP1 | 7:99410169:+_7:99400424:- | Local Inversion | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| DLC1–TPTEP2 | 8:13604537:-_22:38336706:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC138696.1–MOB3A | 8:143251340:+_19:2078679:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC138696.1–ELFN1 | 8:143251340:+_7:1709091:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PLEC–PARP10 | 8:143975177:-_8:143986438:- | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | yes |
| HGH1–CPSF6 | 8:144137958:+_12:69239612:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| RB1CC1–AMN1 | 8:52645702:-_12:31672377:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CAVIN4–MSANTD3-TMEFF1 | 9:100578551:+_9:100576516:+ | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| CAVIN4–MSANTD3-TMEFF1 | 9:100586185:+_9:100498765:+ | Local Rearrangement | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PTGR1–CHD9 | 9:111592926:-_16:53235185:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | yes |
| KIAA1958–SNX30 | 9:112487118:+_9:112804776:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| INIP–C9orf147 | 9:112717987:-_9:112487090:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| ZBTB34–RALGPS1 | 9:126860739:+_9:126962225:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PRRC2B–ATP5PO | 9:131432794:+_21:33904021:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PRRC2B–ANP32B | 9:131439061:+_9:98015364:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| MED27–RAPGEF1 | 9:131853035:-_9:131650949:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | yes |
| AL355987.4–MAN1B1 | 9:136808326:+_9:137088075:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| LINC00032–EQTN | 9:27271927:-_9:27286362:- | Overlapping Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| LINC00032–EQTN | 9:27274090:-_9:27286362:- | Overlapping Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| OSTF1–APP | 9:75088726:+_21:26112146:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| MT-CO3–AL450405.1 | MT:9411:+_6:117998990:+ | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| Z68871.1–LINC00630 | X:102905737:+_X:102816992:+ | Overlapping Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| TMEM164–RTL9 | X:110173453:+_X:110445153:+ | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC073529.1–MID1 | X:11038603:-_X:10567603:- | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC073529.1–MID1 | X:11106901:-_X:10567603:- | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| DDX3X–STK39 | X:41337465:+_2:167964726:- | Inter Chromosomal | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AL050309.1–KLF8 | X:55908800:+_X:56250231:+ | Neighbours | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| NLGN4X–AC110995.1 | X:5844434:-_X:5669606:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| PNPLA4–ANOS1 | X:7912028:-_X:8623670:- | Distant Proximity | 1 | 0 | Inf | 0.0131578 | Inf | 0.8000000 | |
| AC074286.1–AC073636.1 | 2:177094575:-_2:176846377:- | Distant Proximity | 15 | 5 | 0.7396686 | 0.2857924 | Inf | 0.8087205 | |
| SPSB4–PXYLP1 | 3:141066798:+_3:141260123:+ | Neighbours | 204 | 55 | 0.8325058 | 0.5428240 | Inf | 0.8109189 | |
| AC079313.1–NCKAP1L | 12:54353896:+_12:54499355:+ | Neighbours | 3 | 1 | 0.7484239 | 0.0815259 | Inf | 0.8198884 | |
| AC010332.1–ZNF880 | 19:52392788:+_19:52369787:+ | Local Rearrangement | 3 | 1 | 0.7484239 | 0.0815259 | Inf | 0.8198884 | |
| RNF144A–AC013460.1 | 2:7030215:+_2:7421184:+ | Distant Proximity | 3 | 1 | 0.7484239 | 0.0815259 | Inf | 0.8198884 | |
| B3GALT5–AF064860.1 | 21:39605225:+_21:39725838:+ | Overlapping Neighbours | 3 | 1 | 0.7484239 | 0.0815259 | Inf | 0.8198884 | |
| SLC38A9–MTREX | 5:55697846:-_5:55340010:+ | Distant Proximity | 3 | 1 | 0.7484239 | 0.0815259 | Inf | 0.8198884 | |
| AC009315.1–FSIP2 | 2:185483091:+_2:185739346:+ | Distant Proximity | 154 | 43 | 0.8174895 | 0.5395972 | Inf | 0.8349925 | |
| AC012414.4–AC012414.2 | 15:20755930:-_15:20759907:- | Local Rearrangement | 8 | 3 | 0.6597751 | 0.1866294 | Inf | 0.8413667 | |
| MFSD14C–ZNF510 | 9:96918643:-_9:96776245:- | Distant Proximity | 8 | 3 | 0.6597751 | 0.1866294 | Inf | 0.8413667 | |
| CHST9–AQP4 | 18:27024116:-_18:26862596:- | Neighbours | 5 | 2 | 0.6204697 | 0.1262877 | Inf | 0.8535156 | |
| AC120193.1–AC023202.1 | 8:24296154:-_8:24183283:- | Distant Proximity | 5 | 2 | 0.6204697 | 0.1262877 | Inf | 0.8535156 | |
| BNIP3L–DPYSL2 | 8:26408376:+_8:26581969:+ | Neighbours | 5 | 2 | 0.6204697 | 0.1262877 | Inf | 0.8535156 | |
| TMED3–MINAR1 | 15:79314005:+_15:79456098:+ | Neighbours | 7 | 3 | 0.5758904 | 0.1565446 | Inf | 0.8815093 | |
| LINC00869–SEC22B3P | 1:149607554:+_1:148779001:- | Distant Proximity | 2 | 1 | 0.4981146 | 0.0386191 | Inf | 0.8966433 | |
| CSTF3–FBXO3 | 11:33141667:-_11:33742084:- | Distant Proximity | 2 | 1 | 0.4981146 | 0.0386191 | Inf | 0.8966433 | |
| AP002784.1–PANX1 | 11:94189083:+_11:94178369:+ | Local Rearrangement | 2 | 1 | 0.4981146 | 0.0386191 | Inf | 0.8966433 | |
| PSPC1–ZMYM5 | 13:19759323:-_13:19835689:- | Local Rearrangement | 2 | 1 | 0.4981146 | 0.0386191 | Inf | 0.8966433 | |
| USP22–RN7SL1 | 17:21000941:-_14:49586613:+ | Inter Chromosomal | 2 | 1 | 0.4981146 | 0.0386191 | Inf | 0.8966433 | |
| PANTR1–LINC01114 | 2:104851312:-_2:104749489:- | Neighbours | 2 | 1 | 0.4981146 | 0.0386191 | Inf | 0.8966433 | |
| MMP24OS–EDEM2 | 20:35272005:-_20:35142478:- | Neighbours | 2 | 1 | 0.4981146 | 0.0386191 | Inf | 0.8966433 | |
| AC025465.1–LINC01170 | 5:124512257:-_5:124386273:- | Neighbours | 2 | 1 | 0.4981146 | 0.0386191 | Inf | 0.8966433 | |
| ZNRF2P1–FKBP9 | 7:32729009:+_7:32974617:+ | Distant Proximity | 2 | 1 | 0.4981146 | 0.0386191 | Inf | 0.8966433 | |
| OR51S1–TP53I11 | 11:4848669:-_11:44933050:- | Distant Proximity | 6 | 3 | 0.4924414 | 0.1269719 | Inf | 0.9164357 | |
| KHDRBS2-OT1–KHDRBS2 | 6:61652255:-_6:61732764:- | Overlapping Neighbours | 6 | 3 | 0.4924414 | 0.1269719 | Inf | 0.9164357 | |
| LINC01572–PMFBP1 | 16:72284572:-_16:72174070:- | Neighbours | 5 | 3 | 0.4094664 | 0.0980454 | Inf | 0.9453606 | |
| PPP4R3B–CCDC88A | 2:55558775:-_2:55418916:- | Distant Proximity | 7 | 4 | 0.4273438 | 0.1283228 | Inf | 0.9517590 | |
| AL050309.1–KLF8 | X:56014961:+_X:56250231:+ | Neighbours | 7 | 4 | 0.4273438 | 0.1283228 | Inf | 0.9517590 | |
| AL391840.3–SH3BGRL2 | 6:79538843:+_6:79673614:+ | Neighbours | 272 | 75 | 0.6187910 | 0.3493038 | Inf | 0.9596768 | |
| ST6GALNAC5–AL035409.2 | 1:76868742:+_1:77068084:+ | Neighbours | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| AC093423.3–ZNF326 | 1:89843782:+_1:89998110:+ | Neighbours | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| RAB38–AP000676.5 | 11:88149675:-_11:87954906:- | Neighbours | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| TUBA1B–PTMS | 12:49127984:-_12:6770157:+ | Distant Proximity | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| TUBA1A–PTMS | 12:49127984:-_12:6770157:+ | Distant Proximity | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| SMG1–NPIPB13 | 16:18858170:-_16:30245853:- | Distant Proximity | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| LINC01572–PMFBP1 | 16:72249163:-_16:72171268:- | Neighbours | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| LINC01572–PMFBP1 | 16:72267552:-_16:72164916:- | Neighbours | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| PDK1–RAPGEF4 | 2:172670884:+_2:172795025:+ | Distant Proximity | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| ABLIM2–AFAP1 | 4:7983264:-_4:7872080:- | Neighbours | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| KHDRBS2-OT1–KHDRBS2 | 6:61652255:-_6:61697253:- | Overlapping Neighbours | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| FAM155B–EDA | X:69506143:+_X:69957027:+ | Neighbours | 1 | 1 | 0.2489532 | 0.0064235 | Inf | 0.9603563 | |
| LINC01933–AC008571.2 | 5:152270360:+_5:152537704:+ | Distant Proximity | 3 | 3 | 0.2447366 | 0.0435728 | Inf | 0.9837215 | |
| TVP23C–AC005703.3 | 17:15540433:-_17:15416233:- | Neighbours | 1 | 2 | 0.1233715 | 0.0042115 | Inf | 0.9922129 | yes |
| TVP23C-CDRT4–AC005703.3 | 17:15540433:-_17:15416233:- | Neighbours | 1 | 2 | 0.1233715 | 0.0042115 | Inf | 0.9922129 | yes |
| AC074286.1–AC092162.2 | 2:177094575:-_2:176792644:- | Distant Proximity | 1 | 2 | 0.1233715 | 0.0042115 | Inf | 0.9922129 | |
| CRYBB2P1–GRK3 | 22:25459515:+_22:25644592:+ | Neighbours | 1 | 2 | 0.1233715 | 0.0042115 | Inf | 0.9922129 | |
| LINC01933–AC008571.2 | 5:152267355:+_5:152375103:+ | Distant Proximity | 1 | 2 | 0.1233715 | 0.0042115 | Inf | 0.9922129 | |
| MAPT–KANSL1 | 17:45978440:+_17:46094701:- | Local Inversion | 2 | 3 | 0.1629334 | 0.0199570 | Inf | 0.9935909 | |
| B3GALT5–AF064860.1 | 21:39613067:+_21:39725838:+ | Overlapping Neighbours | 2 | 3 | 0.1629334 | 0.0199570 | Inf | 0.9935909 | |
| EFCAB2–KIF26B | 1:245083688:+_1:245366834:+ | Neighbours | 13 | 9 | 0.3382355 | 0.1478283 | Inf | 0.9950241 | |
| PXDC1–AL033523.1 | 6:3737079:-_6:3594535:- | Neighbours | 1 | 3 | 0.0813852 | 0.0031107 | Inf | 0.9984844 | |
| ELAPOR1–ELAPOR2 | 1:109200237:+_7:86891889:- | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| RAP1A–RAP1B | 1:111691417:+_12:68650400:+ | Inter Chromosomal | 0 | 2 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| CROCCP2–AL391832.4 | 1:16625775:-_1:234814281:- | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| WDTC1–MYG1 | 1:27303795:+_12:53306680:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| RCC1–STRAP | 1:28506084:+_12:15894047:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| SSBP3–SSBP2 | 1:54239129:-_5:81440636:- | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| NFIA-AS2–AC099792.1 | 1:60988645:-_1:60826585:- | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AL033530.1–AL691520.1 | 1:68882003:+_1:69013503:+ | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| CADM1–LRP5 | 11:115504271:-_11:68347847:+ | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | yes |
| ZNF195–RPL13A | 11:3370975:-_19:49491425:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| PHF21A–LINC02489 | 11:46076754:-_11:46256541:- | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| MALAT1–DAG1 | 11:65505019:+_3:49530797:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AP003071.5–MYEOV | 11:69135532:+_11:69341510:+ | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| CPSF6–TPTEP2-CSNK1E | 12:69262562:+_22:38336706:- | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | yes |
| SOCS2–TGFBI | 12:93583028:+_5:136063638:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| TMPO–VSIG10 | 12:98528012:+_12:118073992:- | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| NAXD–ING1 | 13:110615647:+_13:110719229:+ | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| TSC22D1–TSC22D2 | 13:44436044:-_3:150458376:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| EFCAB11–AL137230.1 | 14:89931541:-_14:89629136:- | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AC012405.1–AC073941.1 | 15:46410353:+_15:46804641:+ | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AC037433.1–AC009654.1 | 15:60223070:-_15:60074935:- | Neighbours | 0 | 3 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AC138932.3–NOMO1 | 16:14953015:-_16:14894998:+ | Local Inversion | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| HS3ST4–USP6NL | 16:25693151:+_10:11518574:- | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AC009070.1–PRMT2 | 16:81006734:-_21:46643535:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| SMYD4–NASP | 17:1827861:-_1:45584108:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| SUZ12P1–CCDC47 | 17:30769965:+_17:63766194:- | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | yes |
| MAPT–KANSL1 | 17:45962470:+_17:46094701:- | Local Inversion | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| RPL17-C18orf32–RPL17P12 | 18:49491405:-_2:146194373:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| PPP4R1–STXBP3 | 18:9588089:-_1:108782422:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| CNN1–CNN3 | 19:11549469:+_1:94898083:- | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AC123912.1–ZNF493 | 19:21569104:-_19:21405761:+ | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| HECW2–SCAMP2 | 2:196433132:-_15:74848645:- | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| ARMC9–LYRM1 | 2:231240041:+_16:20915556:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| TET3–DGUOK | 2:74003166:+_2:73946719:+ | Local Rearrangement | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| ANKRD36C–AC008268.1 | 2:95884173:-_2:95667917:+ | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| SNAP25–SRP72 | 20:10284772:+_4:56500536:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| EPB41L1–EPB41L2 | 20:36187763:+_6:130895119:- | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AL031686.1–ZNF334 | 20:46474501:-_20:46504740:- | Local Rearrangement | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| CRYBB2P1–GRK3 | 22:25520733:+_22:25661576:+ | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| METTL6–SH3BP5 | 3:15424955:-_3:15304231:- | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| GPR149–DHX36 | 3:154421039:-_3:154316163:- | Neighbours | 0 | 2 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| CCNL1–SMARCA2 | 3:157157023:-_9:2181571:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| RPL22L1–RPL22P22 | 3:170868013:-_X:82506571:- | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| FGF12–AC092966.1 | 3:192727181:-_3:193169464:- | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| ZNF589–FBXW12 | 3:48260939:+_3:48373308:+ | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | yes |
| ERC2–WNT5A | 3:55606780:-_3:55480918:- | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| CAMK2D–PBX3 | 4:113509638:-_9:125960684:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AC053527.2–ALB | 4:73302385:+_4:73404369:+ | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| SEPTIN11–CCNI | 4:76949930:+_4:77066405:- | Local Inversion | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| LINC02200–APC | 5:112632097:+_5:112754873:+ | Neighbours | 0 | 2 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| CTNNA1–CTNNA2 | 5:138887642:+_2:80544982:+ | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AC114316.1–NR2F1-AS1 | 5:92204684:+_5:93563463:- | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AC026780.2–NR2F1-AS1 | 5:92688120:-_5:93411509:- | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| SNAP91–PICALM | 6:83707798:-_11:86031611:- | Inter Chromosomal | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| HOXA1–SKAP2 | 7:27095261:-_7:26844137:- | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AC211476.4–CCDC146 | 7:73072670:+_7:77236947:+ | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| XKR6–LONRF1 | 8:10924634:-_8:12743282:- | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| CASC9–AC100782.1 | 8:75324221:-_8:75029459:- | Neighbours | 0 | 3 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| STK3–VPS13B | 8:98749276:-_8:99134632:+ | Local Inversion | 0 | 2 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| ZNF483–ECPAS | 9:111534353:+_9:111444494:- | Local Inversion | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | yes |
| ABHD17B–CEMIP2 | 9:71862551:-_9:71750385:- | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AC073529.1–MID1 | X:11055936:-_X:10567603:- | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| CLIC2–AC234781.1 | X:155334371:-_X:155335249:- | Local Rearrangement | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| AL050309.1–KLF8 | X:56014961:+_X:56265180:+ | Neighbours | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 | |
| NLGN4X–PUDP | X:6029280:-_X:6706466:- | Distant Proximity | 0 | 1 | 0.0000000 | 0.0000000 | Inf | 1.0000000 |
base_substitutions.als_ctrl.sd <- plot_spectrum(type_occurrences, by = answerals.metadata$condition, CT = FALSE, indv_points = TRUE, error_bars = "stdev") # error bars SD rather than 95% CI
base_substitutions.als_ctrl.sdtb_per_sample <- type_occurrences[, seq_len(6)] %>% tibble::rownames_to_column("sample") %>%
dplyr::mutate(condition = factor(toupper(answerals.metadata$condition), levels = c("CTRL","ALS"))) %>% tidyr::pivot_longer(c(-sample,
-condition), names_to = "variable", values_to = "nmuts") %>%
dplyr::group_by(sample) %>% dplyr::mutate(value = nmuts/sum(nmuts)) %>%
dplyr::ungroup() %>% dplyr::mutate(sub_type = stringr::str_remove(variable,
" .*"), variable = factor(variable, levels = unique(variable)))
tb <- tb_per_sample %>% dplyr::group_by(condition, variable) %>% dplyr::summarise(sub_type = sub_type[[1]],
mean = mean(value), stdev = stats::sd(value), total_individuals = sum(value),
total_mutations = sum(nmuts)) %>% dplyr::mutate(total_individuals = sum(total_individuals),
total_mutations = sum(total_mutations)) %>% dplyr::mutate(sem = stdev/sqrt(total_individuals),
error_95 = ifelse(total_individuals > 1, qt(0.975, df = total_individuals -
1) * sem, NA)) %>% dplyr::ungroup() %>% dplyr::mutate(total_mutations = prettyNum(total_mutations,
big.mark = ","), total_mutations = paste("No. mutations = ",
total_mutations), error_pos = mean)
tb_per_sample = left_join(tb_per_sample, tb[, c("condition", "sub_type", "total_mutations")], by = c("condition", "sub_type"))
base_substitutions.als_ctrl.sd.type <- ggplot(data = tb_per_sample, aes(x = condition, y = value, colour = condition)) +
ggrastr::rasterise(geom_violin(adjust = 1), dpi = 72) +
ggrastr::rasterise(geom_sina(size = 0.5), dpi = 72) +
ggrastr::rasterise(geom_boxplot(aes(fill = condition), colour = "black", width=0.2, alpha = 0.5, outlier.shape = NA), dpi = 72) +
scale_colour_manual(values = c("dodgerblue2", "firebrick2")) + scale_fill_manual(values = c("dodgerblue2", "firebrick2")) +
theme_bw() + xlab("") + ylab("Relative proportions") +
theme_oz() + theme(panel.spacing.x = unit(0.5, "lines"), legend.position = "none") +
facet_wrap(~ sub_type, scales = "free", nrow = 2)
base_substitutions.als_ctrl.sd.typeanswerals.vcfannotate.mutation = answerals.vcfannotate %>% mutate(genetic_group = case_when(mutation == "c9orf72" ~ "C9orf72", mutation == "sod1" ~ "SOD1", mutation == "sporadic" ~ "Sporadic",mutation %in% c("ctrl","iso") ~ "CTRL"), genetic_group = factor(genetic_group, levels = c("CTRL", "Sporadic", "C9orf72", "SOD1"))) %>% #mutation == "fus" ~ "FUS","FUS", mutation == "tardbp" ~ "TARDBP", "TARDBP",
drop_na(genetic_group) %>% # remove all other mutants n < 3.
distinct(dataset_sample, .keep_all = TRUE) %>% select(dataset_sample, total, genetic_group, CONDITION, total_reads, mutation) # keep 1 row per sample
answerals.metadata_genetic_subgroup = answerals.metadata %>% filter(mutation %in% c("ctrl", "iso", "sporadic", "sod1", "c9orf72")) #"fus", "tardbp",
answerals.vcfannotate.samples_no_variants = answerals.metadata_genetic_subgroup$dataset_sample[!answerals.metadata_genetic_subgroup$dataset_sample %in% answerals.vcfannotate.mutation$dataset_sample]
answerals.vcfannotate.mutation.totals = answerals.vcfannotate.mutation %>% distinct(dataset_sample, .keep_all = TRUE) #keep 1 row per sample for total number of variants
# generalised linear model spline
## sporadic
answerals.vcfannotate.mutation.totals.glm.sporadic = glm(data=filter(answerals.vcfannotate.mutation.totals, genetic_group %in% c("Sporadic", "CTRL")), total ~ genetic_group + rms::rcs(total_reads, 3), family = poisson)
summary(answerals.vcfannotate.mutation.totals.glm.sporadic)##
## Call:
## glm(formula = total ~ genetic_group + rms::rcs(total_reads, 3),
## family = poisson, data = filter(answerals.vcfannotate.mutation.totals,
## genetic_group %in% c("Sporadic", "CTRL")))
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -20.781 -7.213 -2.644 2.758 48.707
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.064e+01 3.849e-03 2764.35 <2e-16 ***
## genetic_groupSporadic 1.365e-02 7.146e-04 19.11 <2e-16 ***
## rms::rcs(total_reads, 3)total_reads 4.026e-09 4.936e-11 81.55 <2e-16 ***
## rms::rcs(total_reads, 3)total_reads' -2.007e-09 5.421e-11 -37.02 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 48341 on 241 degrees of freedom
## Residual deviance: 33515 on 238 degrees of freedom
## AIC: 36626
##
## Number of Fisher Scoring iterations: 3
# Coefficients:
# Estimate Std. Error z value Pr(>|z|)
# (Intercept) 1.064e+01 3.849e-03 2764.35 <2e-16 ***
# genetic_groupSporadic 1.365e-02 7.146e-04 19.11 <2e-16 ***
# Violin total variant events
answerals.vcfannotate.mutation.stat <- answerals.vcfannotate.mutation %>% wilcox_test(total ~ genetic_group) %>% add_significance() %>% add_xy_position() %>% filter(group1 == "CTRL") %>%
mutate(p.adj.signif = case_when(group2 == "Sporadic" ~ "****", TRUE ~ p.adj.signif), y.position = case_when(group2 == "Sporadic" ~ 75000, TRUE ~ y.position))
answerals.vcfannotate.mutation.violin <- violin_plot(answerals.vcfannotate.mutation.totals, color_by = "genetic_group", continuous = "total", cols = c("dodgerblue2","firebrick2","forestgreen","gold2","purple","grey"), plot_stats = FALSE, arrow_labels = FALSE, ylims = c(50000,76000), dpi = 72, ylabel = "Number of Variants") +
stat_pvalue_manual(answerals.vcfannotate.mutation.stat, tip.length = 0.01, size = 4, hide.ns = TRUE)
answerals.vcfannotate.mutation.violinipsc_mn_als_datasets.starfusion.fusion_type_n = ipsc_mn_als_datasets.starfusion %>%
add_count(dataset_sample, fusion_type) %>% # count number of fusion types per sample
distinct(dataset_sample, fusion_type, .keep_all = TRUE) %>% select(dataset_sample, fusion_type, n, condition, dataset, total_reads) #keep 1 row per sample fusion type
# add samples with 0 fusions for each fusion type
samples_no_neighbours = ipsc_mn_als_datasets.paired_end.metadata$dataset_sample[!ipsc_mn_als_datasets.paired_end.metadata$dataset_sample %in% pull(filter(ipsc_mn_als_datasets.starfusion.fusion_type_n,fusion_type == "Neighbours"),dataset_sample)]
ipsc_mn_als_datasets.paired_end.metadata.no_neighbours = ipsc_mn_als_datasets.paired_end.metadata %>% filter(dataset_sample %in% samples_no_neighbours) %>% mutate(fusion_type = "Neighbours", n = 0) %>%
select(dataset_sample, n, condition, fusion_type)
samples_no_local_rearrangement = ipsc_mn_als_datasets.paired_end.metadata$dataset_sample[!ipsc_mn_als_datasets.paired_end.metadata$dataset_sample %in% pull(filter(ipsc_mn_als_datasets.starfusion.fusion_type_n,fusion_type == "Local\nRearrangement"),dataset_sample)]
ipsc_mn_als_datasets.paired_end.metadata.no_local_rearrangement = ipsc_mn_als_datasets.paired_end.metadata %>% filter(dataset_sample %in% samples_no_local_rearrangement) %>% mutate(fusion_type = "Local\nRearrangement", n = 0) %>%
select(dataset_sample, n, condition, fusion_type)
samples_no_local_inversion = ipsc_mn_als_datasets.paired_end.metadata$dataset_sample[!ipsc_mn_als_datasets.paired_end.metadata$dataset_sample %in% pull(filter(ipsc_mn_als_datasets.starfusion.fusion_type_n,fusion_type == "Local\nInversion"),dataset_sample)]
ipsc_mn_als_datasets.paired_end.metadata.no_local_inversion = ipsc_mn_als_datasets.paired_end.metadata %>% filter(dataset_sample %in% samples_no_local_inversion) %>% mutate(fusion_type = "Local\nInversion", n = 0) %>%
select(dataset_sample, n, condition, fusion_type)
samples_no_overlapping_neighbours = ipsc_mn_als_datasets.paired_end.metadata$dataset_sample[!ipsc_mn_als_datasets.paired_end.metadata$dataset_sample %in% pull(filter(ipsc_mn_als_datasets.starfusion.fusion_type_n,fusion_type == "Overlapping\nNeighbours"),dataset_sample)]
ipsc_mn_als_datasets.paired_end.metadata.no_overlapping_neighbours = ipsc_mn_als_datasets.paired_end.metadata %>% filter(dataset_sample %in% samples_no_overlapping_neighbours) %>% mutate(fusion_type = "Overlapping\nNeighbours", n = 0) %>%
select(dataset_sample, n, condition, fusion_type)
samples_no_distant_proximity = ipsc_mn_als_datasets.paired_end.metadata$dataset_sample[!ipsc_mn_als_datasets.paired_end.metadata$dataset_sample %in% pull(filter(ipsc_mn_als_datasets.starfusion.fusion_type_n,fusion_type == "Distant\nProximity" ),dataset_sample)]
ipsc_mn_als_datasets.paired_end.metadata.no_distant_proximity = ipsc_mn_als_datasets.paired_end.metadata %>% filter(dataset_sample %in% samples_no_distant_proximity) %>% mutate(fusion_type = "Distant\nProximity" , n = 0) %>%
select(dataset_sample, n, condition, fusion_type)
samples_no_inter_chromosomal = ipsc_mn_als_datasets.paired_end.metadata$dataset_sample[!ipsc_mn_als_datasets.paired_end.metadata$dataset_sample %in% pull(filter(ipsc_mn_als_datasets.starfusion.fusion_type_n,fusion_type == "Inter\nChromosomal"),dataset_sample)]
ipsc_mn_als_datasets.paired_end.metadata.no_inter_chromosomal = ipsc_mn_als_datasets.paired_end.metadata %>% filter(dataset_sample %in% samples_no_inter_chromosomal) %>% mutate(fusion_type = "Inter\nChromosomal", n = 0) %>%
select(dataset_sample, n, condition, fusion_type)
ipsc_mn_als_datasets.starfusion.fusion_type_n = bind_rows(ipsc_mn_als_datasets.starfusion.fusion_type_n, ipsc_mn_als_datasets.paired_end.metadata.no_neighbours, ipsc_mn_als_datasets.paired_end.metadata.no_local_rearrangement, ipsc_mn_als_datasets.paired_end.metadata.no_local_inversion,
ipsc_mn_als_datasets.paired_end.metadata.no_overlapping_neighbours, ipsc_mn_als_datasets.paired_end.metadata.no_distant_proximity, ipsc_mn_als_datasets.paired_end.metadata.no_inter_chromosomal) %>%
mutate(CONDITION = factor(toupper(condition), levels = c("CTRL","ALS")),
fusion_type = factor(fusion_type, levels = c("Local\nInversion", "Local\nRearrangement", "Neighbours", "Overlapping\nNeighbours", "Distant\nProximity", "Inter\nChromosomal")))
### Inter_Chromosomal
glm_starfusion_Inter_Chromosomal = glm(data = filter(ipsc_mn_als_datasets.starfusion.fusion_type_n, fusion_type == "Inter\nChromosomal"), n ~ CONDITION + dataset + rms::rcs(total_reads, 3), family=poisson)
summary(glm_starfusion_Inter_Chromosomal)##
## Call:
## glm(formula = n ~ CONDITION + dataset + rms::rcs(total_reads,
## 3), family = poisson, data = filter(ipsc_mn_als_datasets.starfusion.fusion_type_n,
## fusion_type == "Inter\nChromosomal"))
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.5908 -0.3609 -0.2594 0.3255 1.6615
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.547e-01 1.269e+00 -0.122 0.902967
## CONDITIONALS 6.354e-01 1.717e-01 3.700 0.000216 ***
## datasetcatanese -1.414e-01 4.205e-01 -0.336 0.736669
## datasetdafinca.c9orf72 1.712e-01 1.099e+00 0.156 0.876214
## datasetdafinca.tardbp 1.176e-01 9.441e-01 0.125 0.900858
## datasetdesantis 2.212e-01 8.711e-01 0.254 0.799528
## datasetkiskinis 2.404e+00 1.037e+00 2.317 0.020488 *
## datasetneurolincs.diMN -3.735e-02 3.225e-01 -0.116 0.907791
## datasetneurolincs.iMN -4.341e-01 7.340e-01 -0.591 0.554279
## datasetwang 1.406e+00 7.545e-01 1.863 0.062466 .
## rms::rcs(total_reads, 3)total_reads -3.379e-10 2.106e-08 -0.016 0.987194
## rms::rcs(total_reads, 3)total_reads' -3.008e-09 1.343e-08 -0.224 0.822832
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 229.815 on 131 degrees of freedom
## Residual deviance: 37.707 on 120 degrees of freedom
## (264 observations deleted due to missingness)
## AIC: 363.08
##
## Number of Fisher Scoring iterations: 4
# Coefficients:
# Estimate Std. Error z value Pr(>|z|)
# (Intercept) -1.546e-01 1.269e+00 -0.122 0.903002
# CONDITIONALS 6.354e-01 1.717e-01 3.700 0.000216 ***
ipsc_mn_als_datasets.starfusion.fusion_type.stat <- ipsc_mn_als_datasets.starfusion.fusion_type_n %>% group_by(fusion_type) %>% t_test(n ~ CONDITION) %>% mutate(p.signif = c("ns","ns","ns","ns","ns","***"), y.position = 24)
ipsc_mn_als_datasets.starfusion.fusion_type.violin <- ggplot(ipsc_mn_als_datasets.starfusion.fusion_type_n, aes(x = CONDITION, y = n, colour = CONDITION)) +
# ggrastr::rasterise(geom_violin(adjust = 2), dpi = 72) +
ggrastr::rasterise(geom_sina(size = 0.5), dpi = 72) +
ggrastr::rasterise(geom_boxplot(aes(fill = CONDITION), colour = "black", width=0.2, alpha = 0.5, outlier.shape = NA), dpi = 72) +
scale_colour_manual(values = c("dodgerblue2", "firebrick2")) + scale_fill_manual(values = c("dodgerblue2", "firebrick2")) +
theme_oz() + theme(legend.position = "none", plot.title = element_text(hjust = 0.5), plot.subtitle = element_text(hjust = 0.5), panel.border = element_blank(), axis.ticks = element_line(colour = "black") ) +
facet_wrap(~ fusion_type, scales = "free", nrow = 2) + labs(y = "Number of Fusion Events", x = "") +
stat_pvalue_manual(ipsc_mn_als_datasets.starfusion.fusion_type.stat, label = "p.signif", tip.length = 0.01, size = 4, hide.ns = TRUE)
ipsc_mn_als_datasets.starfusion.fusion_type.violin# histogram
ipsc_mn_als_datasets.starfusion.fusion_type.histogram = ggplot(ipsc_mn_als_datasets.starfusion.fusion_type_n, aes(x=n, color=CONDITION, fill=CONDITION)) +
geom_histogram(alpha=0.5, position="identity", binwidth = 1)+
scale_color_manual(values=c("dodgerblue2", "firebrick2"))+ scale_fill_manual(values=c("dodgerblue2", "firebrick2"))+
facet_wrap(~ fusion_type, scales = "free", nrow = 2) + theme_oz() #+ ggtitle("Zeros filled")
ipsc_mn_als_datasets.starfusion.fusion_type.histogram# Sporadic
ipsc_mn_als_datasets.starfusion.sporadic = read_csv(here(proj_path,"rnafusion/ipsc_mn_als_datasets.starfusion.csv")) %>%
mutate(CONDITION = factor(toupper(condition), levels = c("CTRL","ALS")), fusion_type = factor(fusion_type, levels = c("Local\nInversion", "Local\nRearrangement", "Neighbours", "Overlapping\nNeighbours", "Distant\nProximity", "Inter\nChromosomal")),
genetic_group = case_when(mutation == "c9orf72" ~ "C9orf72", mutation == "sod1" ~ "SOD1", mutation == "sporadic" ~ "Sporadic", mutation == "fus" ~ "FUS", mutation == "tardbp" ~ "TARDBP", mutation %in% c("ctrl","iso") ~ "CTRL"),
genetic_group = factor(genetic_group, levels = c("CTRL", "Sporadic", "SOD1", "C9orf72", "FUS", "TARDBP"))) %>%
filter(dataset %in% c("answerals","neurolincs.diMN"), mutation %in% c("ctrl","iso","sporadic")) %>% left_join(multiqc_rseqc_read_distribution.tsv)
ipsc_mn_als_datasets.starfusion.sporadic.n = ipsc_mn_als_datasets.starfusion.sporadic %>%
add_count(dataset_sample) %>% # count number of fusion per sample
distinct(dataset_sample, .keep_all = TRUE) %>% select(dataset_sample, n, CONDITION, genetic_group, mutation, dataset, total_reads) #keep 1 row per sample
ipsc_mn_als_datasets.starfusion.sporadic.n.stats = tibble(group1 = "CTRL", group2 = "Sporadic", p.signif = "ns", y.position = 40, xmin = 1, xmax = 2)
ipsc_mn_als_datasets.starfusion.sporadic.violin <- violin_plot(ipsc_mn_als_datasets.starfusion.sporadic.n, color_by = "genetic_group", continuous = "n", cols = c("dodgerblue2", "firebrick2"), plot_stats = FALSE, arrow_labels = FALSE, ylims = c(0,43), dpi = 72, ylabel = "Number of Fusion Events") +
stat_pvalue_manual(ipsc_mn_als_datasets.starfusion.sporadic.n.stats, tip.length = 0.01, size = 4, hide.ns = TRUE)
# C9orf72
ipsc_mn_als_datasets.starfusion.c9orf72 = read_csv(here(proj_path,"rnafusion/ipsc_mn_als_datasets.starfusion.csv")) %>%
mutate(CONDITION = factor(toupper(condition), levels = c("CTRL","ALS")), fusion_type = factor(fusion_type, levels = c("Local\nInversion", "Local\nRearrangement", "Neighbours", "Overlapping\nNeighbours", "Distant\nProximity", "Inter\nChromosomal")),
genetic_group = case_when(mutation == "c9orf72" ~ "C9orf72", mutation == "sod1" ~ "SOD1", mutation == "sporadic" ~ "Sporadic", mutation == "fus" ~ "FUS", mutation == "tardbp" ~ "TARDBP", mutation %in% c("ctrl","iso") ~ "CTRL"),
genetic_group = factor(genetic_group, levels = c("CTRL", "Sporadic", "SOD1", "C9orf72", "FUS", "TARDBP"))) %>%
filter(dataset %in% c("answerals","neurolincs.diMN","catanese","dafinca.c9orf72","neurolincs.iMN","sommer"), mutation %in% c("ctrl","iso","c9orf72")) %>% left_join(multiqc_rseqc_read_distribution.tsv)
ipsc_mn_als_datasets.starfusion.c9orf72.n = ipsc_mn_als_datasets.starfusion.c9orf72 %>%
add_count(dataset_sample) %>% # count number of fusion per sample
distinct(dataset_sample, .keep_all = TRUE) %>% select(dataset_sample, n, CONDITION, genetic_group, mutation, dataset, total_reads) #keep 1 row per sample
# add samples with 0 fusions
# glm_starfusion.c9orf72 = glm(data = ipsc_mn_als_datasets.starfusion.c9orf72.n, n ~ genetic_group + dataset + rms::rcs(total_reads, 3), family=poisson)
# summary(glm_starfusion.c9orf72)
# Coefficients:
# Estimate Std. Error z value Pr(>|z|)
# (Intercept) 2.783e+00 5.216e-01 5.336 9.50e-08 ***
# CONDITIONALS 2.401e-01 6.037e-02 3.978 6.96e-05 ***
# Violin
ipsc_mn_als_datasets.starfusion.c9orf72.n.stats = tibble(group1 = "CTRL", group2 = "C9orf72", p.signif = "****", y.position = 40, xmin = 1, xmax = 2)
ipsc_mn_als_datasets.starfusion.c9orf72.violin <- violin_plot(ipsc_mn_als_datasets.starfusion.c9orf72.n, color_by = "genetic_group", continuous = "n", cols = c("dodgerblue2", "forestgreen"), plot_stats = FALSE, arrow_labels = FALSE, ylims = c(0,43), dpi = 72, ylabel = "Number of Unique Fusion Events") +
stat_pvalue_manual(ipsc_mn_als_datasets.starfusion.c9orf72.n.stats, tip.length = 0.01, size = 4, hide.ns = TRUE)
# TARDBP
ipsc_mn_als_datasets.starfusion.tardbp = read_csv(here(proj_path,"rnafusion/ipsc_mn_als_datasets.starfusion.csv")) %>%
mutate(CONDITION = factor(toupper(condition), levels = c("CTRL","ALS")), fusion_type = factor(fusion_type, levels = c("Local\nInversion", "Local\nRearrangement", "Neighbours", "Overlapping\nNeighbours", "Distant\nProximity", "Inter\nChromosomal")),
genetic_group = case_when(mutation == "c9orf72" ~ "C9orf72", mutation == "sod1" ~ "SOD1", mutation == "sporadic" ~ "Sporadic", mutation == "fus" ~ "FUS", mutation == "tardbp" ~ "TARDBP", mutation %in% c("ctrl","iso") ~ "CTRL"),
genetic_group = factor(genetic_group, levels = c("CTRL", "Sporadic", "SOD1", "C9orf72", "FUS", "TARDBP"))) %>%
filter(dataset %in% c("answerals","dafinca.tardbp","smith"), mutation %in% c("ctrl","iso","tardbp")) %>% left_join(multiqc_rseqc_read_distribution.tsv)
ipsc_mn_als_datasets.starfusion.tardbp.n = ipsc_mn_als_datasets.starfusion.tardbp %>%
add_count(dataset_sample) %>% # count number of fusion per sample
distinct(dataset_sample, .keep_all = TRUE) %>% select(dataset_sample, n, CONDITION, genetic_group, mutation, dataset, total_reads) #keep 1 row per sample
# add samples with 0 fusions
ipsc_mn_als_datasets.paired_end.metadata.tardbp = ipsc_mn_als_datasets.paired_end.metadata %>% filter(dataset %in% c("answerals","dafinca.tardbp","smith"), mutation %in% c("ctrl","iso","tardbp"))
ipsc_mn_als_datasets.starfusion.samples_no_fusions.tardbp = ipsc_mn_als_datasets.paired_end.metadata.tardbp$dataset_sample[!ipsc_mn_als_datasets.paired_end.metadata.tardbp$dataset_sample %in% ipsc_mn_als_datasets.starfusion.tardbp.n$dataset_sample]
ipsc_mn_als_datasets.paired_end.metadata.no_fusions.tardbp = ipsc_mn_als_datasets.paired_end.metadata.tardbp %>% filter(dataset_sample %in% ipsc_mn_als_datasets.starfusion.samples_no_fusions.tardbp) %>%
left_join(multiqc_rseqc_read_distribution.tsv) %>%
mutate(CONDITION = factor(toupper(condition), levels = c("CTRL","ALS")), n = 0, genetic_group = case_when(mutation == "c9orf72" ~ "C9orf72", mutation == "sod1" ~ "SOD1", mutation == "sporadic" ~ "Sporadic", mutation == "fus" ~ "FUS", mutation == "tardbp" ~ "TARDBP", mutation %in% c("ctrl","iso") ~ "CTRL"),
genetic_group = factor(genetic_group, levels = c("CTRL", "Sporadic", "SOD1", "C9orf72", "FUS", "TARDBP"))) %>% select(dataset_sample, n, CONDITION, mutation, dataset, total_reads, genetic_group)
ipsc_mn_als_datasets.starfusion.tardbp.n = bind_rows(ipsc_mn_als_datasets.starfusion.tardbp.n, ipsc_mn_als_datasets.paired_end.metadata.no_fusions.tardbp)
# Violin
ipsc_mn_als_datasets.starfusion.tardbp.n.stats = tibble(group1 = "CTRL", group2 = "TARDBP", p.signif = "ns", y.position = 40, xmin = 1, xmax = 2)
ipsc_mn_als_datasets.starfusion.tardbp.violin <- violin_plot(ipsc_mn_als_datasets.starfusion.tardbp.n, color_by = "genetic_group", continuous = "n", cols = c("dodgerblue2", "purple"), plot_stats = FALSE, arrow_labels = FALSE, ylims = c(0,43), dpi = 72, ylabel = "Number of Fusion Events") +
stat_pvalue_manual(ipsc_mn_als_datasets.starfusion.tardbp.n.stats, tip.length = 0.01, size = 4, hide.ns = TRUE)
# FUS
ipsc_mn_als_datasets.starfusion.fus = read_csv(here(proj_path,"rnafusion/ipsc_mn_als_datasets.starfusion.csv")) %>%
mutate(CONDITION = factor(toupper(condition), levels = c("CTRL","ALS")), fusion_type = factor(fusion_type, levels = c("Local\nInversion", "Local\nRearrangement", "Neighbours", "Overlapping\nNeighbours", "Distant\nProximity", "Inter\nChromosomal")),
genetic_group = case_when(mutation == "c9orf72" ~ "C9orf72", mutation == "sod1" ~ "SOD1", mutation == "sporadic" ~ "Sporadic", mutation == "fus" ~ "FUS", mutation == "tardbp" ~ "TARDBP", mutation %in% c("ctrl","iso") ~ "CTRL"),
genetic_group = factor(genetic_group, levels = c("CTRL", "Sporadic", "SOD1", "C9orf72", "FUS", "TARDBP"))) %>%
filter(dataset %in% c("catanese","desantis"), mutation %in% c("ctrl","iso","fus")) %>% left_join(multiqc_rseqc_read_distribution.tsv)
ipsc_mn_als_datasets.starfusion.fus.n = ipsc_mn_als_datasets.starfusion.fus %>%
add_count(dataset_sample) %>% # count number of fusion per sample
distinct(dataset_sample, .keep_all = TRUE) %>% select(dataset_sample, n, CONDITION, genetic_group, mutation, dataset, total_reads) #keep 1 row per sample
# add samples with 0 fusions
# Violin
ipsc_mn_als_datasets.starfusion.fus.n.stats = tibble(group1 = "CTRL", group2 = "FUS", p.signif = "ns", y.position = 40, xmin = 1, xmax = 2)
ipsc_mn_als_datasets.starfusion.fus.violin <- violin_plot(ipsc_mn_als_datasets.starfusion.fus.n, color_by = "genetic_group", continuous = "n", cols = c("dodgerblue2", "grey"), plot_stats = FALSE, arrow_labels = FALSE, ylims = c(0,43), dpi = 72, ylabel = "Number of Fusion Events") +
stat_pvalue_manual(ipsc_mn_als_datasets.starfusion.fus.n.stats, tip.length = 0.01, size = 4, hide.ns = TRUE)
# SOD1
ipsc_mn_als_datasets.starfusion.sod1 = read_csv(here(proj_path,"rnafusion/ipsc_mn_als_datasets.starfusion.csv")) %>%
mutate(CONDITION = factor(toupper(condition), levels = c("CTRL","ALS")), fusion_type = factor(fusion_type, levels = c("Local\nInversion", "Local\nRearrangement", "Neighbours", "Overlapping\nNeighbours", "Distant\nProximity", "Inter\nChromosomal")),
genetic_group = case_when(mutation == "c9orf72" ~ "C9orf72", mutation == "sod1" ~ "SOD1", mutation == "sporadic" ~ "Sporadic", mutation == "fus" ~ "FUS", mutation == "tardbp" ~ "TARDBP", mutation %in% c("ctrl","iso") ~ "CTRL"),
genetic_group = factor(genetic_group, levels = c("CTRL", "Sporadic", "SOD1", "C9orf72", "FUS", "TARDBP"))) %>%
filter(dataset %in% c("answerals","neurolincs.diMN", "kiskinis","wang"), mutation %in% c("ctrl","iso","sod1")) %>% left_join(multiqc_rseqc_read_distribution.tsv)
ipsc_mn_als_datasets.starfusion.sod1.n = ipsc_mn_als_datasets.starfusion.sod1 %>%
add_count(dataset_sample) %>% # count number of fusion per sample
distinct(dataset_sample, .keep_all = TRUE) %>% select(dataset_sample, n, CONDITION, genetic_group, mutation, dataset, total_reads) #keep 1 row per sample
# add samples with 0 fusions
# Violin
ipsc_mn_als_datasets.starfusion.sod1.n.stats = tibble(group1 = "CTRL", group2 = "SOD1", p.signif = "****", y.position = 40, xmin = 1, xmax = 2)
ipsc_mn_als_datasets.starfusion.sod1.violin <- violin_plot(ipsc_mn_als_datasets.starfusion.sod1.n, color_by = "genetic_group", continuous = "n", cols = c("dodgerblue2", "gold2"), plot_stats = FALSE, arrow_labels = FALSE, ylims = c(0,43), dpi = 72, ylabel = "Number of Fusion Events") +
stat_pvalue_manual(ipsc_mn_als_datasets.starfusion.sod1.n.stats, tip.length = 0.01, size = 4, hide.ns = TRUE)
plot_grid(ipsc_mn_als_datasets.starfusion.sporadic.violin, ipsc_mn_als_datasets.starfusion.c9orf72.violin, ipsc_mn_als_datasets.starfusion.sod1.violin, ipsc_mn_als_datasets.starfusion.tardbp.violin, ipsc_mn_als_datasets.starfusion.fus.violin, nrow = 2)